Download The microbial view of marine biogeochemical cycles

International Workshop
The microbial view of marine biogeochemical cycles
19-21 May 2010
Banyuls-sur-Mer, France
Organised by the Laboratoire d’Océanographie Microbienne (LOMIC)
Supported by
Observatoire Océanologique de Banyuls (OOB)
Université Pierre et Marie Curie (Paris6)
Centre National de la Recherche Scientifique (CNRS)
Scientific Committee:
Ingrid Obernosterer (Chair), Laboratoire d’Océanographie Microbienne, Banyuls, France
Josep Gasol, Institut de Ciències del Mar, CSIC, Barcelona, Spain
Gerhard Herndl, Dept. of Marine Biology, Univ. of Vienna, Austria
David Kirchman, School of Marine Science and Policy, Univ. of Delaware, Lewes, USA
Mary Ann Moran, Dept. of Marine Sciences, Univ. of Georgia, Athens, USA
Jarone Pinhassi, School of Pure and Applied Natural Sciences, Univ. of Kalmar, Sweden
Marcelino Suzuki, Laboratoire d’Océanographie Microbienne, Banyuls, France
Foreword
Over the past two decades, a suite of culture-independent molecular based techniques
has allowed us to determine microbial community composition at different phylogenetic
levels in the ocean. These techniques have given insight into the dominant microbial groups
present at varying temporal and spatial scales. More recent high throughput approaches such
as pyrosequencing have the potential to reveal the so-called “rare biosphere” of microbial
communities and thus to nearly unlock what we once considered a black box. However, the
functional role of individual microbial groups in biogeochemical cycles remains thus far
poorly understood. Single-cell analysis and quantitative determination of particular genes and
their expression are presently the most common approaches to link microbial community
structure to function. The extraordinary advances in (meta)genomics, (meta)transcriptomics,
and (meta)proteomics present additional new approaches that have the potential to provide
detailed insight into the metabolic capabilities and thus functional roles of natural microbial
communities. Together, these techniques offer us the possibility to address questions at
different phylogenetic levels, from natural microbial communities to strains with entirely
sequenced genomes.
The objective of this workshop is to discuss how these various approaches can
contribute to address major, but thus far unresolved issues in marine biogeochemistry. Focus
will be put on the questions “What level of phylogenetic diversity is an appropriate target if
we are to better understand the functional role of microbes in marine biogeochemical cycles?”
and “How can we integrate the “-omics” sciences to investigate functional groups in
relationship to biogeochemical cycles?”
Sixty-four aquatic microbial ecologists, marine biogeochemists and molecular
biologists from 14 countries will be present during this meeting. The 32 oral and 22 poster
presentations will discuss the link between microbial diversity, metabolism and function, and
marine biogeochemical cycles of various elements.
Ingrid Obernosterer
Banyuls-sur-mer, May 3 2010
Workshop Program
WEDNESDAY, MAY 19
14:00h Welcome and Introduction by Ingrid Obernosterer
14:30h-15:00h Keynote Lecture by David Kirchman: Community structure and function of
heterotrophic bacteria in the oceanic carbon cycle
15:00h-15:30h Keynote Lecture by Jarone Pinhassi: Ecological roles of proteorhodopsin
phototrophy in marine bacteria
Session 1 Bacterial metabolism and solar radiation
Chairs: D. Kirchman and J. Pinhassi
Lami R., N.J. West, P. Lebaron and D.L. Kirchman : Distribution and expression of SAR11
proteorhodopsins
Jeffrey W.H., J.D. Pakulski, A.J. Baldwin, J.P. Kase, J.A. Moss, F. Joux, and P.J. Neale:
Spatial patterns of light stimulated bacterial heterotrophic production
16:10-16-40h Coffee Break
Session 1 Bacterial metabolism and solar radiation
Vila-Costa M., S. Sharma, M.A. Moran and E.O. Casamayor.: Comparison of diel gene
expression profiles in an oligotrophic high-altitude lake and two marine systems through
metranscriptomics
Cottrell M., L. Fauteux, P.A. del Giorgio and D. Kirchman: Photoheterotrophy in Quebec
lakes
Session 2 The Fe- and DMS-cycles
Chairs: D. Kirchman and J. Pinhassi
Green D., S. Amin, M. Hart, W. Sunda, F. Küpper and C. Carrano: Bacterial-algal mutualism
and iron supply
Toulza E., A. Tagliabue, L. Bopp, Blain S and G. Piganeau: Can we link metagenome gene
content and iron supply in the ocean ?
Blain S., A. Devez, M. Fourquez, L. Intertaglia, T. Jouenne, A. Schauman, I. Schalk, V.
Goeffroy and I. Obernosterer: Impact of iron limitation on the metabolism and proteom of
some marine heterotrophic bacteria
Johnston A.W.B., J.D. Todd, A.R.J. Curson, M.J. Sullivan and M. Kirkwood.: The organisms,
genes, pathways and regulation of dimethyl sulfide production from
dimethylsulfoniopropionate – a surfeit of biodiversity
19:00h Aperitif and Dinner
THURSDAY, MAY 20
9:00h-9:30h Keynote Lecture by Mary Ann Moran: A Biogeochemist's Guide to Quantitative
Comparative Metatranscriptome Analysis
9:30h-10:00h Keynote Lecture by Gerhard Herndl: Distribution of C and N cycling in the
North Atlantic: functional gene abundance versus biogeochemical rate measurements.
Session 3 Rare microbes
Chairs: M.A. Moran and G. Herndl
Lamy D., H. Agogué, P. Neal, M. Sogin and G. Herndl: Bacterial assemblage composition in
the North Atlantic Ocean revealed by massively parallel sequencing
Galand P.E., E.O. Casamayor, D. Kirchman and C. Lovejoy: Biogeography of the rare Arctic
microbes
10:40h-11:00h Coffee Break
Session 3 Rare microbes
Ghiglione J.-F. and A. Murray: Comparison of massively parallel deep sequencing and
molecular profiling to evaluate the seasonal changes in Sub-Antarctic and Antarctic marine
bacterioplankton communities
Montoya J. Emerging horizons in biodiversity and ecosystem functioning research
Session 4 The N-cycle
Chairs: M.A. Moran and G. Herndl
Sintes E., K. Bergauer, D. De Corte and G.J. Herndl: Archaeal amoA: new insights into the
diversity and biogeography of Archaeal ammonia oxidizers
Fernández C., L. Farias and O. Ulloa: Anaerobic nitrogen fixation: molecular and
biogeochemical approaches
Biegala I., A.-F. Deton, S. Bonnet and P. Raimbault.: Importance of diazotrophic
picocyanobacteria in marine ecosystem functioning (South-West Pacific)
12:40h-14:00h Lunch break
Session 5 Linking bacteria to phytoplankton
Chair: I. Obernosterer
Simon M., S. Hahnke, H.-A. Giebel, H. Osterholz and T. Brinkhoff: Drivers of organic matter
turnover in the sea – some examples from the Roseobacter clade
Sarmento H. and J.M. Gasol: Specific phytoplankton – bacteria interactions through dissolved
organic carbon
Laghdass M., S. Blain, M. Besseling, P. Catala, C. Guieu and I. Obernosterer: Impact of
Saharan dust deposition on the bacterial diversity and activity in the NW Mediterranean Sea
Giebel H.-A., D. Kalhöfer, S. Voget, T. Brinkhoff and M. Simon: The Roseobacter RCA
cluster – its occurrence, diversity and potential significance
Ly J., J.C. Kromkamp and K.C. Timmermans: Effects of phosphorus limitation on marine
natural phytoplankton community structure and function
15:45h-16:15h Coffee Break
16:15h-18:30h Poster Session
19:00h Workshop Dinner
FRIDAY, MAY 21
9:00h-9:30h Keynote Lecture by Josep Gasol: Growth and activity rates of bacterial groups:
can we infer generalizations?
9:30h-10:00h Keynote Lecture by Marcelino Suzuki: In situ gene expression by marine
bacterioplankton at high phylogenetic resolution
10:00h-10:30h Coffee Break
Session 5 Bacterial growth
Chairs: J. Gasol and M. Suzuki
Koblizek M., O. Prasil and B. van Mooy: How fast do marine bacteria grow?
Ferrera I., J.M. Gasol, M. Sebastian, E. Hojerova and M. Koblizek: Manipulation of top-down
pressure and its effects on the growth rates of different bacterial functional and phylogenetic
groups
Teira E., S. Martínez-García, C. Lønborg and X.A. Álvarez-Salgado: Growth rates of different
phylogenetic bacterioplankton groups in a coastal upwelling system
Session 6 Adaptation and Evolution
Chairs: J. Gasol and M. Suzuki
Talarmin A., F. VanWambeke, P. Catala, C. Courties and P. Lebaron: Functional diversity of
bacterioplankton across the oligotrophic Mediterranean Sea assessed by flow cytometry, cell
sorting and FISH techniques
West N., M. Suzuki and P. Lebaron: A novel clade of Prochlorococcus found in HNLC
waters in the South Pacific Ocean
Logares R., E. Lindström, S. Langenheder, J. Laybourn-Parry, L. Tranvik, S. Bertilsson and
K. Rengefors: Different salinities Influence Microbial Community Composition and evolution
in Coastal Antarctic Lakes
Poster Session
1-Agogué H., M. Brink, J. Dinasquet and G. J. Herndl: Pronounced latitudinal and vertical
gradients of putatively nitrifying Archaea in the dark realm of the North Atlantic
2-Akram N., J. Forsberg, J. M. González and J. Pinhassi: Effect of light on proteorhodopsincontaining marine “heterotrophic” bacteria (Vibrio spp.)
3-Alonso C., N. Musat, M. Kuypers and R. Amann: Incorporation of photosynthetically
derived carbon by marine bacteria: first insights into NanoSIMS results
4-Alonso-Sáez L., J. Pinhassi, J. Pernthaler and J.M. Gasol: Leucine-to-carbon empirical
conversion factor experiments: a look at the role of bacterial community composition
5-Bergauer K., E. Sintes, J. van Bleijswijk, and G.J. Herndl: Abundance of autotrophic
bacteria and archaea in the deep north atlantic determined by q-pcr
6-Boeuf D., M. Cottrell, D. Kirchman, P. Lebaron and C. Jeanthon: Abundance and Diversity
of Aerobic Anoxygenic Phototrophic Bacteria in the Beaufort Sea
7-Brauer V. S., de Jonge V. N., Buma A. G. J. and F. J. Weissing: Is the distribution of marine
nitrogen fixation related to temperature?
8-Boutrif M., M. Garel, C. Panagiotopoulos and C. Tamburini: Pressure Effect on the
degradation of Marine Extracellular Polymeric Substances by Deep Sea prokaryotes at the
DYFAMED site (NW Mediterranean Sea)
9-Coll-Lladó M., S.G. Acinas and C. Pedrós-Alió: Transcriptome Fingerprinting: an
approach to explore gene expression patterns in marine microbial communities
10-Díez-Vives C. , J.M. Gasol, B. Díez, V. Balagué, T. Pommier, C. Pedrós-Alió and S.G.
Acinas: insights on diversity and dynamics of bacteroidetes co-existing populations in the
northwestern mediterranean sea
11-Fourquez M., P. Catala, I. Obernosterer and S. Blain: IRON bioavailability for marine
bacteria: a single cell approach
12-Gledhill M., E. Mawji, A. Milton, G. Tarran, M. V. Zubkov, G. Wolff, A. Thompson, and
E. P. Achterberg: Production and occurrence of siderophores along AMT transects
13-Grim S., B. J. Campbell and D. L. Kirchman: Actively replicating bacteria in the MidAtlantic Bight and Sargasso Sea
14-Lai C.-C. J. and F.-K. Shiah: Temperature effects on variation of community respiration
15-Landa M., Blain, S., Batailler N., Caparros J., Catala P., Devez, A., Laghdass, M. Oriol, L.
and I. Obernosterer: Bioavailability of dissolved organic matter and bacterial diversity:
Insights from chemostat culture experiments
16-Lin C.H. M., F.-K. Shiah and T.-Y. Ho: Seasonal succession of phytoplankton
composition in Fei-Tsui reservoir
17-Manes C-L. de O., N.J. West, S. Rapenne and P. Lebaron: Dynamic bacterial communities
on reverse-osmosis membranes in a full-scale desalination plant
18-Molina V., C. Fernandez and L. Farias: Ammonium and nitrite oxidation (de) coupling in
the euphotic zone
19-Nielsdottir M. C., T. S. Bibby, C. M. Moore, R. Sanders, D. J. Hinz, R. Korb, M.
Whitehouse and E. P. Achterberg The seasonal variation of iron stress in the Scotia Sea
20-Rowan K., S.T. Wilson, M.C. Hart, D. H. Green, and A. D. Hatton: The role of faecal
pellet micro-environments in oceanic methane production
21-Salter I., R.S. Lampitt, A.E.S.Kemp, G.A. Wolff, C.M. Moore, J. Holtvoeth and M.T.
Hernandez-Sanchez: Diatom flux assemblages from a naturally iron fertilized bloom:
Implications for carbon cycling in the present day and glacial ocean
22-Varela M.M., V. Balagué, A. Bode, A. Calvo-Díaz, Á. Cid, J. Gasol, E. Marañón and X.Á. G. Morán: Bacterial assemblage structure and carbon metabolism across an Atlantic
latitudinal transect
PRONOUNCED LATITUDINAL AND VERTICAL GRADIENTS
ARCHAEA IN THE DARK REALM OF THE NORTH ATLANTIC
OF IN PUTATIVELY NITRIFYING
AGOGUÉ H.1,2, M. BRINK1, J. DINASQUET1 AND G. J. HERNDL1, 3
1
Department of Biological Oceanography, Royal Netherlands Institute for Sea Research (NIOZ), PO
BOX 59, 1790 AB Den Burg, Netherlands
2
Institut du Littoral et de l’Environnement, UMR LIENSs 6250, CNRS-Université de la Rochelle,
France
3
Department of Marine Biology, Faculty of Life Sciences, University of Vienna, Austria
Aerobic nitrification of ammonia to nitrite and nitrate is one of the major bioelemental
transformations in the sea. Catalyzed by the enzyme ammonia monooxygenase, the ability to oxidize
ammonia, was though until recently, to be driven only by few members of Bacteria. The recent
isolation of ammonia oxidizing Crenarchaeota Nitrosopumilus maritimus revealed the existence of
ammonia monooxygenase genes in mesophilic Archaea. Since then, evidence accumulated that marine
Crenarchaeota, the most abundant group of Archaea in pelagic waters, are capable of ammonia
oxidation. To determine the distribution of ammonia monooxygenase subunit A (amoA) gene copy
numbers from the surface to the bathypelagic layers of the North Atlantic water column (from 63°N to
5°S), the abundance of 16S rRNA genes and archaeal and bacterial amoA genes were determined. The
analyses revealed that the abundance of the gene encoding for the archaeal amoA is decreasing
drastically with depth especially in the eastern subtropical Atlantic. This coincides with the lower
nutrient concentration of the deep waters in the southern parts of the North Atlantic and the older age
of the deep-water masses there. Our data demonstrate that the activity of the Crenarchaeota is closely
linked to the major water masses of the North Atlantic and does not just follow depth-related trends
and that most bathypelagic Crenarchaeota are not autotrophic ammonia oxidizers: most likely, they
utilize organic matter and hence live heterotrophically.
EFFECT OF LIGHT ON PROTEORHODOPSIN-CONTAINING
BACTERIA (VIBRIO SPP.)
MARINE “HETEROTROPHIC”
AKRAM N.1, J. FORSBERG1, J. M. GONZÁLEZ2 AND J. PINHASSI1
1
Marine Microbiology, School of Natural Sciences, Linnaeus University, 9182 Kalmar, Sweden
Departamento de Microbiologia y Biologia Celular, Facultad de Farmacia, Universidad de La
Laguna, 38206 La Laguna, Tenerife, Spain
2
Proteorhodopsin caught hold of the marine scientific community’s imagination and attention
back in year 2000 when metagenomic analysis of bacterioplankton community samples showed these
photoproteins to be ubiquitously distributed throughout the world oceans. But the mysteries
surrounding this tantalizing protein have not been fully unveiled – most notably, no single ecological
role has been possible to assign to proteorhodopsin and it has been proposed to have ‘an array of
physiological roles’. This is in stark contrast to the relatively well characterized biochemistry of the
proteorhodopsin molecule itself. Nevertheless, research the last few years has provided a few glimpses
about the role of light for stimulating e.g. growth, gene expression and anaplerotic carbon dioxide
fixation in proteorhodopsin-containing bacteria. Our study is an attempt to decipher the ecological role
of phototrophy in members of the marine genus Vibrio, consisting of heterotrophic bacteria of which
some only recently were discovered to have the potential for phototrophy. Survival of Vibrio sp.
AND4 cells harvested from exponential or mid-stationary phases was investigated under light and
dark conditions. Light-stimulated survival of cells only from stationary phase indicated regulation of
proteorhodopsin gene expression through different growth phases, rather than constitutive expression.
Screening of Vibrio isolates revealed proteorhodopsin also in another marine strain, SCB39, although
this isolate reacted differently to light. These results indicate that proteorhodopsins even in very
closely related species may have different ecological roles.
INCORPORATION OF PHOTOSYNTHETICALLY
INSIGHTS INTO NANOSIMS RESULTS
DERIVED CARBON BY MARINE BACTERIA: FIRST
ALONSO C.1, N. MUSAT2, M. KUYPERS2 AND R. AMANN2
1
2
Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
Max Planck Institute for Marine Microbiology, Bremen, Germany
The Río de la Plata estuary, situated between Argentina and Uruguay, is the world’s largest
estuary. This system, besides entailing a highly productive area, is particularly relevant for the global
carbon budget, acting as a CO2 sink, especially during spring and summer. Thus, it is a particularly
appealing ecosystem for studying the role of major bacterial groups in the carbon cycle. In this work,
an experiment was performed by adding 13C labeled bicarbonate to whole water samples. Incubations
were run for 24 hours at in situ temperature and light conditions. Samples were taken after 2, 4, 8, 12
and 24 hours of incubation for analysis of the 13C incorporation into bacterial cells using NanoSIMS.
Alphaproteobacteria, Gammaproteobacteria and Bacteroidetes, the three major bacterial groups
present in the samples, were identified by halogen in situ hybridization (HISH) with rRNA-targeted
oligonucleotide probes. Preliminary results indicate that both, the percentage of Bacteroidetes cells
enriched in 13C and the enrichment factor increased with incubation time, achieving their maximum
after 24 h. On the contrary, the proportion of alphaproteobacterial cells enriched in 13C and their
corresponding enrichment factor decreased along incubation time. A high proportion (>60%) of cells
in all three groups were 13C enriched after 24 h of incubation; the highest value was found among
Bacteroidetes (85%). After 24 hours of incubation Bacteroidetes and Gammaproteobacteria exhibited
very similar average values for the factor of enrichment, while Alphaproteobacteria exhibited much
lower values. In summary, the major bacterial groups of the Río de la Plata estuary exhibited different
incorporation patterns of photosynthetically derived products. Given the pronounced differences in the
distribution of these groups along this system, this could have impacts on the functioning of the carbon
cycle in the different portions of the estuary.
LEUCINE-TO-CARBON
EMPIRICAL CONVERSION FACTOR EXPERIMENTS : A LOOK AT THE
ROLE OF BACTERIAL COMMUNITY COMPOSITION
ALONSO-SÁEZ L.1,2, J. PINHASSI3, J. PERNTHALER4 AND J. M. GASOL1
1
Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Spain
Centro oceanográfico de Gijón, Instituto Español de Oceanografía, Spain
3
Marine Microbiology, School of Natural Sciences, Linnaeus University, Kalmar, Sweden
4
Limnological station, Institute of Plant biology, University of Zurich, Switzerland
2
The suitability of applying empirical conversion factors (eCFs) to determine bacterial biomass
production remains unclear because seawater cultures (SWCs) are usually overtaken by phylotypes
that are not abundant in situ. While eCFs vary across environments, it has not been tested whether
differences in eCFs are driven by changes in bacterial community composition (BCC) or by in situ
environmental conditions. We carried out SWCs throughout a year to analyse the correlation between
eCFs and BCC, analysed by catalyzed reporter deposition fluorescence in situ hybridization.
Gammaproteobacteria usually dominated SWCs, but their abundance exhibited a wide range (25-73%
of cell counts) and significantly increased with inorganic nutrient enrichment. Bacteroidetes were less
abundant but increased up to 40% of cells counts in winter SWCs, when in situ chlorophyll a was
high. The correlations between eCFs and the abundance of the main broad phylogenetic groups
(Gamma-, Alphaproteobacteria and Bacteroidetes) were significant, albeit weak, while more specific
groups (Alteromonadaceae and Rhodobacteraceae) were not significantly correlated. Our results show
that the frequent development of the fast-growing group Alteromonadaceae in SWCs does not
strongly drive variations in eCFs. Rather, the results imply that there is an interconexion between
environmental conditions and the growth of specific phylotypes in determining eCFs.
ABUNDANCE
OF AUTOTROPHIC BACTERIA AND ARCHAEA IN THE DEEP NORTH ATLANTIC
DETERMINED BY Q-PCR
BERGAUER K.1, E. SINTES2, J. VAN BLEIJSWIJK2 AND G.J. HERNDL1,2
1
University of Vienna, Ecology Center, Dept. of Marine Biology, A-1090 Vienna, Austria
Dept. of Biological Oceanography, Royal Netherlands Institute for Sea Research (NIOZ), 1790AB
Den Burg, The Netherlands
2
Prokaryotes are the main players in the biogeochemical carbon cycling in aquatic ecosystems.
Apart from the Calvin-Bassham-Benson cycle as prevalent autotrophic pathway in Bacteria and
eukaryotes, four alternative metabolic mechanisms of CO2 fixation are found exclusively in
prokaryotes. We aimed at determining the relative abundance of chemoautotrophic Archaea and
Bacteria in the meso- and bathypelagic ocean and link the gene abundance indicative for
chemoautrotrophy to inorganic carbon fixation in the dark. For developing suitable primer sets for
quantitative PCR (Q-PCR) on the prokaryotic autotrophy, we focused on acetyl CoA carboxylase
(ACCase), a key enzyme participating inter alia in the 3-hydroxypropionate/malyl-CoA and its
modified 3-hydroxypropionate/4-hydroxybutyrate cycle. Hence the oligonucleotide primers target the
respective encoding accC gene. Besides its catalytic function in autotrophic pathways, the enzyme
ACCase is a mediator in the biosynthesis of fatty acids and therefore ubiquitously distributed in a wide
range of organisms. However, due to the lack of fatty acids in archaeal lipids, the enzyme is supposed
to function in other metabolic pathways, potentially allowing to determine the proportional
contribution of Archaea and Bacteria to overall microbial production in the pelagic realm. Q-PCR with
these sets of primers was applied to samples from the Arctic Sea and the North Atlantic and related to
bacterial and archaeal amoA copy numbers and inorganic carbon uptake rates. The number of accC
gene copy numbers decreased from the oxygen minimum layer to the lower mesopelagic layer in the
North Atlantic and remained fairly constant throughout the water column in the Arctic. Based on our
results with the newly developed primers, we conclude that deep ocean prokaryotes might have a
larger potential of autotrophy than assumed hitherto.
IMPORTANCE OF DIAZOTROPHIC PICOCYANOBACTERIA
FUNCTIONING (SOUTH-WEST PACIFIC)
IN MARINE ECOSYSTEM
BIEGALA I.C.1, A.-F. DETON1, S. BONNET2 AND P. RAIMBAULT3
1
Laboratoire d’Océanographie et de Biogéochimie, UMR 6535 LOPB, Centre d’Océanologie de
Marseille, rue de la Batterie des Lions, 13007 Marseille, France
2
Laboratoire d’Océanographie et de Biogéochimie, UMR 6535 LOPB, Centre d’Océanologie de
Marseille, Campus de Luminy case 901, Cedex 9, 13288 Marseille, France
3
Laboratoire de Microbiologie Géochimie et Ecologie Marine, UMR 6117, Campus de Luminy case
901, Cedex 9, 13288 Marseille, France
It is now more and more recognized that the unicellular diazotrophic cyanobacteria play an
important role in marine nitrogen and carbon cycles, although these organisms are still not taken into
account in global biogeochemical budgets and models. In this study we quantified unicellular
diazotrophic cyanobacteria (UCYN2-FIX lineage) using specific whole cell hybridization technique
(TSA-FISH) within picoplanktonic, nanoplanctonic and larger size fractions. Surprisingly a significant
population of diazotrophic pico-cyanobacteria was discovered in every size fractions and over a large
range of nutrient concentrations. These diazotrophs were numerically dominating the UCYN2-FIX
community at 97% and 98% in coastal and oceanic environments respectively. In these environments
N2-fixation from the < 10 µm size fraction contributed to 74% of total nitrogen fixation. Along the
oceanic equatorial transect diazotrophy could explain from 2% to 22% of N source in the Pacific
HNLC and oligotrophic warm pool waters, respectively.
Phylogenetic analysis were done on 16SrRNA with specific UCYN2-FIX primers and
confirmed the targeted picocyanobacteria belong to Group-A from the UCYN2-FIX community.
Although most of the diazotrophic picocyanobacteria were free living a third of them were either
associated to particles or intracellular of non-thecate dinoflagellates. These associations were mainly
observed in nutrient rich environment where particulate organic matters were highly concentrated. In
these rich environments (urbanized coastline or equatorial upwelling) diazotrophic picocyanobacteria
were either passively trapped on inert particles or may be chemically attracted towards these
microenvironments which can provide essential nutrient for growth. The frequent association with
non-thecate dinoflagellates reveal either a recent ingestion, or more probably symbiotic associations.
Further work should be done to characterize better these associations.
ABUNDANCE AND DIVERSITY OF AEROBIC ANOXYGENIC PHOTOTROPHIC BACTERIA IN THE
BEAUFORT SEA
BOEUF D.1,2, M. COTTRELL3, D. KIRCHMAN3, P. LEBARON4,5 AND C. JEANTHON1,2
1
UPMC Univ Paris VI, UMR 7144, Station Biologique, BP 74, 29682 Roscoff, France
CNRS, UMR 7144, Groupe Plancton Océanique, Station Biologique, BP 74, 29682 Roscoff, France
3
School of Marine Science and Policy, University of Delaware, Lewes, Delaware 19958, USA
4
UPMC Univ Paris 06, UMR 7621, LOMIC, Observatoire Océanologique, F-66651 Banyuls/mer,
France
5
CNRS, UMR 7621, LOMIC, Observatoire Océanologique, F-66651, Banyuls/mer, France
2
Photoheterotrophy, which is the ability to utilize organic substrates and harvest light energy,
occurs in a broad range of microbes, including aerobic anoxygenic phototrophic bacteria (AAPB),
proteorhodopsin-containing bacteria (PRB), and cyanobacteria. The hybrid metabolism of
photoheterotrophs (respiration and phototrophy) will probably make them key players in the Arctic
ocean where solar radiation increases in the aquatic environment due to a decrease in summer ice
cover. Abundance of cyanobacteria in Arctic waters is generally low and little is known about the
abundance and diversity of AAPB and PRB. To give new insights into the ecological significance of
the latter functional groups in Arctic waters, we conducted an extensive study in the MacKenzie
river/Beaufort Sea system in August 2009 onboard the Canadian research icebreaker Amundsen.
We first analyze the abundance and diversity of AAPB using infrared epifluorescence
microscopy and cultural and molecular approaches, respectively. Very low relative abundances of
AAPB were generally recorded across the transect covering the North Pacific waters, the Bering and
Beaufort Seas (< 1% of the total prokaryotic community). The highest contributions of AAPB were
obtained in samples subjected to Arctic rivers and the MacKenzie plume (between 6% to 14.2% of the
total prokaryotes). A low cultural diversity was observed among our 145 AAPB isolates screened
using T-RFLP. The 16S rRNA sequences of the different T-RFLP groups are being sequenced and
their phylogenetic diversity will be presented. The molecular diversity of AAPB is actually analyzed
by comparing TTGE profiles of the pufM gene, involved in bacteriochlorophyll (BChl a) synthesis,
and sequencing of pufM clone libraries. Amplifications were obtained only in samples that yielded the
highest cellular abundances, suggesting that AAPB are dominated by freshwater ecotypes. Sequencing
of pufM gene libraries is underway to test this hypothesis.
I MPACT
OF IRON LIMITATION ON THE METABOLISM AND PROTEOM OF SOME MARINE
HETEROTROPHIC BACTERIA
BLAIN S. 1,2, A. DEVEZ1,2, M. FOURQUEZ1,2, L. INTERTAGLIA1,3, T. JOUENNE4, A. SCHAUMAN4, I.
SCHALK5, V. GOEFFROY5 AND I. OBERNOSTERER1,2
1
UPMC Univ Paris 06, UMR 7621, LOMIC, UMS 2348, Observatoire Océanologique, F-66651
Banyuls/mer, France
2
CNRS, UMR 7621, LOMIC, Observatoire Océanologique, F-66651, Banyuls/mer, France
3
CNRS, UMS 2348, Observatoire Océanologique, F-66651, Banyuls/mer, France
4
CNRS, UMR 6270, Université de Rouen, F-76821 Mont-Saint-Aignan, Cedex, France
5
CNRS-Université de Strasbourg, FRE3211, ESBS, Illkirch, France
Iron limitation of phytoplankton in vast areas of the ocean is now well documented, but the
case of heterotrophic bacteria remains less explored and puzzling. For example, in High Nutrient Low
Chlorophyll regions, previous studies report contradictory results indicating that iron or carbon might
be the proximate factor of control. The aim of our study was to get new insights into this issue. We
examined how iron limitation impacts major bacterial processes (e.g. growth, respiration) and related
biogeochemical properties (e.g. bacterial growth efficiency) of three different strains belonging to
Gammaproteobacteria. A mechanistic basis for the understanding of these observations is provided by
the comparative analysis of the total proteomes of these strains grown under iron-deficient and ironlimited conditions, and the comparison of bulk parameters (e.g. elemental quota, biovolumes) for ironlimited and non- limited cells.
P RESSURE E FFECT ON THE DEGRADATION OF M ARINE E XTRACELLULAR POLYMERIC
SUBSTANCES BY DEEP SEA PROKARYOTES AT THE DYFAMED SITE (NW MEDITERRANEAN
SEA)
BOUTRIF M., M. GAREL, C. PANAGIOTOPOULOS AND C. TAMBURINI
Université de la Méditerranée, Centre d'Océanologie de Marseille, LMGEM UMR 6117 CNRS –
INSU, Campus de Luminy, Case 901, 13288 Marseille, Cedex 9, France
The interactions between prokaryotes and marine dissolved organic matter (DOM) play a
major role in the global carbon cycle. DOM is (technically) divided into high molecular weight
(HMW-DOM) and low molecular weight (LMW-DOM) size classes. A large part of the HMW-DOM
is composed of carbohydrates (50-60% of HMW-DOM). In this work, we focus on the ability of deepsea prokaryotes to degrade exopolysaccharides (considered to be HMW-DOM) radiolabeled with
tritium (3H-EPS). We synthesized 3H-EPS and incubated them with deep-sea samples from the
DYFAMED time-series station (NW Mediterranean Sea) under in situ pressure conditions to estimate
the deep-sea prokaryotic capacity to degrade HMW-DOM. Simultaneously, we examined 3H-Glucose
assimilation rates and prokaryotic production (3H-Leucine). Degradation rates were higher under in
situ pressure than at atmospheric conditions. These results also suggested that EPS may sustain
prokaryotic production in the deep-sea waters. Using Micro-CARD-FISH, in order to determine the
contribution of each prokaryotic group to the degradation of 3H-EPS, we observed that at the surface,
14% of total Bacteria cells degrade the 3H-EPS. This percentage decreases with depth to 6% of relative
participation. In contrast, the participation of Euryarchaea on degradation of 3H EPS increases with
depth (from 11% of total euryarchaea at the surface to 59% at 2000m). For Crenarchaea, the relative
percentage of cells assimilating 3H EPS is very weak (between 1 and 3%). These major results indicate
that deep-sea Euryarchaea more actively degrade semi-labile compounds in the deep sea than other
prokaryotic groups.
IS THE DISTRIBUTION OF MARINE NITROGEN FIXATION RELATED TO TEMPERATURE?
BRAUER V. S.1,2,3, DE JONGE V. N.4, BUMA A. G. J.1 AND F. J. WEISSING2
1
Ocean Ecosystems, Centre for Ecological and Evolutionary Studies, University of Groningen,
Kerklaan 30, 9751 NN Haren, The Netherlands
2
Theoretical Biology, Centre for Ecological and Evolutionary Studies, University of Groningen,
Kerklaan 30, 9751 NN Haren, The Netherlands
3
Present address: Aquatic Microbiology, University of Amsterdam, Nieuwe Achtergracht 127, 1018
WS Amsterdam, The Netherlands
4
Institute of Estuarine & Coastal Studies, University of Hull, Hull HU6 7RX, UK
The metabolic theory of ecology (MTE) is an intriguing but controversial theory that tries to
explain ecological patterns at all scales on the basis of first principles. Temperature plays a pivotal role
in this theory. According to MTE, the Arrhenius relationship that describes the effect of temperature
on biochemical reactions extends to a ‘universal temperature dependence’ that encompasses all kinds
of processes and scales up to the cellular, the organismal, and the community level. In this study we
test the prediction that community growth rate is temperature dependent in an Arrhenius-like way.
First, we performed a literature review of the scanty data on the temperature dependence of the rates of
metabolism, photosynthesis and growth of communities. In contrast to the predictions of MTE, the
community activation energies did not cluster around 0.32 eV, the activation energy of photosynthesis
and primary production or around 0.65 eV, the activation energy of metabolism. However, in none of
the published studies the conditions were sufficiently controlled to allow firm conclusions. We
therefore also performed replicated and controlled experiments using natural assemblages of marine
plankton. As predicted by MTE, the maximal growth rates of community biomass increased linearly in
an Arrhenius plot, with a slope close to 0.32 eV. However, a diversity of other models for the
temperature dependence of community growth rates fit our data equally well. Hence, our results are at
best a weak confirmation of MTE.
TRANSCRIPTOME FINGERPRINTING: AN APPROACH
TO EXPLORE GENE EXPRESSION
PATTERNS IN MARINE MICROBIAL COMMUNITIES
COLL-LLADÓ M., S.G. ACINAS AND C. PEDRÓS-ALIÓ
Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC, Barcelona,
Catalonia, Spain
Fingerprinting DNA approaches such DGGE, t-RFLP or ARISA are widely used to compare
diversity and explore dynamics of the marine microbial communities allowing the comparison of a
large number of samples at a relatively low cost. However, information about dynamics of the genes
expressed by such communities is barely known. Specific gene expression can be successfully
detected through quantitative RT-PCR, and microarrays are helpful tools to detect the expression level
of a set of known genes. In addition, the 454 pyrosequencing technology has been recently applied to
analyze marine microbial communities transcriptomes. However, this technology is still very costly
and provides short sequences that many times cannot be assigned to any known gene. In this sense,
alternative approaches are needed to systematically compare and detect gene expression patterns at
high-throughput level and with reasonable time and money costs.
We have adapted the differential display technique based on the PCR amplification of expressed
transcripts to interrogate natural microbial eukaryotic communities. Unlike other techniques,
differential display does not require prior knowledge of the mRNA sequences to be detected. We have
used a set of arbitrary primers coupled with a fluorescence labeled primer targeting the poly(A) tail of
the eukaryotic mRNA, with further detection of the resulting labeled cDNA products in an automated
genetic analyzer. Comparing the electropherogram patterns from several samples, we obtain a pattern
with peaks that represent environment-specific transcripts. This Transcriptome Fingerprinting
Analysis (TFA) has been optimized by testing the sensitivity of the method for different RNA
concentrations, and the reproducibility of the gene expression patterns with increasing time after
sampling. We observed that time did not alter the patterns of gene expression significantly as long as
samples were kept in ice, for the picoeukaryotic transcripts retrieved at least up to 8 hours after
sampling with several specific primer combinations. Finally, our approach was used in the Blanes Bay
Microbial Observatory during two diel cycles both in open sea and in coastal waters. Our results show
that TFA is a promising approach to explore the dynamics of global gene expression patterns and to
reveal specific differences in transcripts among different samples and/or environmental conditions.
PHOTOHETEROTROPHY IN QUÉBEC LAKES
COTTRELL M. T.1, L. FAUTEUX2, P. DEL GIORGIO2 AND D. L. KIRCHMAN1
1
2
School of Marine Science and Policy, University of Delaware, Lewes, DE 19958 USA
University of Québec at Montreal, Montreal H3C 3P8 Canada
Prokaryotic microbes that rely on photoheterotrophic metabolism consume organic materials
and harvest light energy, which presents challenges when attempting to place them in existing food
web models. The current framework includes two distinct compartments for phototrophic microbes
that produce organic materials and heterotrophic microbes that consume organic materials. In order
to learn where photoheterotrophs fit in aquatic food webs it is necessary to understand their
biogeographical patterns, the environmental conditions that control their abundance and diversity, and
their underlying ecological significance. Our work focuses on the role of photoheterotrophic microbes
in freshwaters and uses a unique set of analytical tools for examining these microbes in the lakes of
southern Québec, the Laurentian region north of Montreal and boreal lakes in the taiga regions of
northern Québec. These lakes vary in several environmental properties (e.g. trophic status, DOC
concentrations, color and turbidity) that are hypothesized to affect photoheterotroph abundance and
diversity. We are using 454 pyrosequencing of genes that are unique to photoheterotrophs and 16S
rRNA genes that are found in all prokaryotes in order to test hypotheses about community dynamics
and environmental controls of photoheterotrophic microbes. Understanding the biogeography,
including the large-scale spatial patterns along environmental gradients and patterns of seasonal
succession are essential first steps towards assessing the potentially distinct impacts of
photoheterotrophs on biogeochemical processes in freshwaters.
INSIGHTS ON DIVERSITY AND DYNAMICS OF BACTEROIDETES CO-EXISTING POPULATIONS IN
THE NORTHWESTERN MEDITERRANEAN SEA
DÍEZ-VIVES C1. , J.M. GASOL1, B. DÍEZ1, V. BALAGUÉ1, T. POMMIER2, C. PEDRÓS-ALIÓ1 AND S.G.
ACINAS1
1
2
Dep. de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Spain
Ecosystmes Lagunaires, Université Montpellier II - CC093, 34 095 Montpellier Cedex 5, France
Marine Bacteroidetes contribute up to 30% of total marine bacterioplankton and play a
relevant role in the degradation of particulate organic matter. Many representatives of this group have
gliding motility and the capacity to degrade polymers, possibly allowing them to grow on detritus or
algal cell particles using the polymeric compounds as carbon and energy sources. Genomes of
Bacteroidetes have shown the presence of proteorhodopsins indicating a potential phototrophic
function and revealing potential alternative ecological strategies. Despite their abundance and
ecological relevance, little is known about the populations of Bacteroidetes co-existing in the ocean.
Probes and primers specific for Bacteroidetes have been previously described for FISH (CF319,
CFB560) and DGGE (CFB555, Cyt1020R) approaches respectively, but we decided to design of a
new, marine Bacteroidetes-specific primer (CF418F) based on: (i) the increasing number of sequences
available in databases, (ii) the lack of specificity of some of the primers currently in use and (iii) to
avoid the nested PCR step needed for the CF555 and Cyt1020R primers for DGGE analyses. In silico
test of the CF418F primer with the latest RDPII database (Release 10, March 2010 with 461183 good
quality and >1200bp sequences) resulted in 48049 hits of a total of 23154 Bacteroidetes-sequences,
with a 48% of coverage. Even if this primer is not covering all Bacteroidetes, it is highly specific for
some marine Bacteroidetes groups such as the family Flavobacteriaceae with 71% of coverage and
presents very few out-group hits. This primer was tested on pure cultures and DGGE band sequences
demonstrated its 100% specificity with all sequences recovered being Bacteroidetes. We explored the
genetic heterogeneity (microdiversity) and dynamics of marine Bacteroidetes using DGGE profiles
and the partial sequencing of the 16S rRNA genes at four different scales: (i) the temporal series with
monthly sampling carried out at a surface coastal station: Blanes Bay Microbial Observatory along a
two year period (2007-2008), (ii) a horizontal profile along a transect from coastal to offshore open
surface waters, (iii) vertical profiles at four stations covering from surface waters down to 2000m
depth and (iv) we explored the differences among free-living and attached marine Bacteroidetes
assemblages retrieved from 0.22 µm and (GF/A) pore size filters throughout a year. Bacteroidetes
were found in most of the water samples and exhibited high diversity with a maximum at the DCM,
and presented recurrent seasonal patterns.
MANIPULATION OF TOP-DOWN PRESSURE AND ITS EFFECTS ON THE GROWTH RATES OF
DIFFERENT BACTERIAL FUNCTIONAL AND PHYLOGENETIC GROUPS
FERRERA I.1, J. M. GASOL1, M. SEBASTIÁN1, E. HOJEROVA2, AND M. KOBLIZEK2
1
2
Dpt. Biologia Marina i Oceanografia. Institut de Ciències del Mar. Barcelona, Catalunya, Spain
Institute of Microbiology, Trebon, Czech Republic
Aerobic anoxygenic phototrophs (AAPs) are a ubiquitous part of the marine microbial
communities. Data from the Atlantic Ocean and the Baltic Sea have shown that these
bacteriochlorophyll-containing bacteria grow at rates much higher than those of the total community.
We first studied their abundance and dynamics at the Blanes Bay Microbial Observatory (BBMO,
coastal Western Mediterranean) where, based on diel changes of bacteriochlorophyll a, we estimated
the AAP community to grow at rates of 1.1 to 1.5 day-1, which is much faster than the rates reported
for the bulk heterotrophic bacterial community of that environment (6-yr. average±SE, 0.16±0.02 d-1).
Despite their growth rates above those of other bacteria, AAPs accounted for only 3-8% of total
prokaryote abundance. We studied this phenomenon by performing experiments of top-down
manipulation in which the pressure of predators and viruses was reduced. We calculated the growth
rates of AAP and compared them to those of different phylogenetic groups (Bacteroidetes, the
alfaproteobacterial groups Roseobacter and SAR11, and Gammaproteobacteria and its subgroup
Alteromonas). In these experiments, AAPs presented growth rates between 2 and more than 3
divisions per day, whereas the average growth rate for total heterotrophic bacteria was approximately
one division per day. The phylogenetic groups Roseobacter and Gammaproteobacteria, which include
members of the AAP bacteria, showed similar growth rates (1-3 divisions per day). However, the
group that showed the fastest growth was Alteromonas, although typically accounts for a very low
percentage of the prokaryotic community of the BBMO. Bacteroidetes, which on average constitute
ca. 11% of the bacterial community in the study site, showed intermediate growth rates (1-2 divisions
per day). The slower growths in all treatments were those of the SAR11 group which, however, has
been shown to dominate year-round in the NW Mediterranean surface waters and seems to be the most
abundant bacterial group in the world’s oceans. These results indicate that the role that some minor
groups, such as the AAP among others, may play in the recycling of organic matter in the ocean is
more important than what their abundances alone would predict.
ANAEROBIC NITROGEN FIXATION: MOLECULAR
AND BIOGEOCHEMICAL APPROACHES
FERNÁNDEZ C.1, 2,3, L. FARIAS3,4 , AND O. ULLOA3,4
1
UPMC Univ Paris 06, UMR 7621, LOMIC, Observatoire Océanologique, F-66651 Banyuls/mer,
France
2
CNRS, UMR 7621, LOMIC, Observatoire Océanologique, F-66651, Banyuls/mer, France
3
Centro de Investigación Oceanográfica en el Pacífico Sur-Oriental (FONDAP-COPAS), Universidad
de Concepción, Casilla 160-C, Concepción, Chile
4
Laboratorio de Procesos Oceanográficos Física y Clima, Universidad de Concepción, Casilla 160-C,
Concepción, Chile
Nitrogen fixation is an essential process by which atmospheric dinitrogen gas is biologically
transformed to ammonia, compensating for global nitrogen losses that occur through denitrification
and anammox. The current view is that inputs and losses of nitrogen via these processes are spatially
separated in the ocean. However, using a stable isotope approach (15N2 assimilation), we explored the
occurrence of Nitrogen fixation in the water column of the permanent upwelling off Peru and northern
Chile (12 - 20ºS), a globally important nitrogen sink, driven by subsurface oxygen deficient
conditions. Our results showed active nitrogen fixation at rates going from 0.02 to 3.5 nmol L-1 d-1
with higher contributions of “new nitrogen” coming from the suboxic layer of the OMZ (51 - 697
mmol m-2 d-1) compared to the oxic-euphotic layer (2.3 – 9.89 mmol m-2 d-1). Phylogenetic analyses of
dinitrogenase reductase genes sequences revealed the presence of diazotrophic prokaryotic
picoplankton might be able of performing anaerobic diazotrophic activity. Our results thus
demonstrate the occurrence of nitrogen fixation in surface nutrient-rich coastal upwelling waters and
coincide with nitrogen losses through denitrification and anammox in both time and space.
IRON BIOAVAILABILITY FOR MARINE BACTERIA: A SINGLE CELL APPROACH
FOURQUEZ M.1,2, P. CATALA1,2, I. OBERNOSTERER1,2 AND S. BLAIN1,2
1
UPMC Univ Paris 06, UMR 7621, LOMIC, Observatoire Océanologique, F-66651 Banyuls/mer,
France
2
CNRS, UMR 7621, LOMIC, Observatoire Océanologique, F-66651, Banyuls/mer, France
Heterotrophic bacteria are key players in the biogeochemical cycle of iron in the marine
environment. They modify the chemical speciation and therefore the bioavailability of iron, and they
compete for the access to iron with other microorganisms. The capability of different bacterial groups
to access various chemical forms of iron is, however, ignored thus far. Over the past few years
microautoradiography was successfully applied to link bacterial diversity to the cycling of elements
such as C, P and S. The aim of our study is to develop a similar approach based on the radioisotope
55
Fe. We will present the first results of this technique applied to bacterial strains (Alteromonas
macleodeii) grown under iron-controlled conditions, and to a natural community of heterotrophic
bacteria collected in the NW Mediterranean Sea. We will discuss the potential, the difficulties and the
limits of microautoradiography using 55Fe in the marine environment.
BIOGEOGRAPHY OF THE RARE ARCTIC MICROBES
GALAND P.E.1,2,3, E.O. CASAMAYOR4, D. KIRCHMAN3 AND C. LOVEJOY5
1
Department of Continental Ecology-Limnology, Centre d’Estudis Avancats de Blanes–CSIC, Blanes,
Spain
2
UPMC Univ Paris 06, FRE 3350, LECOB, Observatoire Océanologique, F-66651 Banyuls/mer,
France
3
CNRS, FRE 3350, LECOB, Observatoire Océanologique, F-66651, Banyuls/mer, France
4
School of Marine Science and Policy, University of Delaware, Lewes, DE, USA
5
Québec-Océan, Département de Biologie, and Institut de Biologie Intégrative et des Systèmes,
Université Laval, Québec, QC, Canada
Understanding the role of microbes in the oceans has focused on taxa that occur in high
abundance; yet most of the marine microbial diversity is largely determined by a long tail of lowabundance taxa. This rare biosphere may have a cosmopolitan distribution because of high dispersal
and low loss rates, and possibly represents a source of phylotypes that become abundant when
environmental conditions change. However, the true ecological role of rare marine microorganisms is
still not known. Here, we use pyrosequencing to describe the structure and composition of the rare
biosphere and to test whether it represents cosmopolitan taxa or whether, similar to abundant
phylotypes, the rare community has a biogeography. Our examination of 740,353 16S rRNA gene
sequences from 32 bacterial and archaeal communities from various locations of the Arctic Ocean
showed that rare phylotypes did not have a cosmopolitan distribution but, rather, followed patterns
similar to those of the most abundant members of the community and of the entire community. The
distribution of communities was explained by the hydrography of the Arctic Ocean and subsequent
circulation of its water masses. Water masses probably act as physical barriers limiting the dispersal
and controlling the diversity of microbes in the ocean. We conclude that the rare biosphere has a
biogeography and that its tremendous diversity is most likely subjected to ecological processes such as
selection, speciation, and extinction.
GROWTH AND ACTIVITY RATES OF BACTERIAL GROUPS: CAN WE INFER GENERALIZATIONS ?
GASOL J.M.
Institut de Ciències del Mar, ICM-CSIC, E-08003 Barcelona, Catalunya, Spain
Linking the role that marine bacterioplankton play in the carbon cycle with the structure of the
bacterial community is a relevant step in our understanding of how oceans work and of the relevance
that microbial diversity has in biogeochemical cycling. It can be approached in different ways, and one
of these is the assignement of general ecological roles to all the bacteria that belong to a specific
bacterial group. In other words, the identification of common ecological traits among the members of
specific groups. Groups are determined according to the availability of group-specific fluorescent in
situ hybridization (FISH) probes, at the level of domain, class, families, or even clades (e.g. SAR11).
These traits and their variation can shed light on fundamental questions in biology, including why
organisms live where they do and how they will respond to global change, but can also be used by
ocean modellers if the bacterial black box is to be open into smaller boxes. Here we review published
experiments using the MAR-FISH technique to detect general patterns in the utilization of simple
model compounds by specific bacterial groups. We have compiled all available data, including some
unpublished of our own, to test whether the study-specific patterns hold also at a larger scale of
analysis. We also compare the intrinsic growth rates of the different marine bacterioplankton groups in
situ, and in the absence of predators or viruses, to stablish the range of potential growth rates of the
diverse groups and test whether there are trends consistent across studies. Our results show repetitive
patterns in the ecological strategy of some groups and no clear conclusions for some other groups.
COMPARISON OF MASSIVELY PARALLEL DEEP SEQUENCING AND MOLECULAR PROFILING TO
EVALUATE THE SEASONAL CHANGES IN SUB-ANTARCTIC AND ANTARCTIC MARINE
BACTERIOPLANKTON COMMUNITIES
GHIGLIONE J.F.1,2 AND A. MURRAY3
1
UPMC Univ Paris 06, UMR 7621, LOMIC, Observatoire Océanologique, F-66651 Banyuls/mer,
France
2
CNRS, UMR 7621, LOMIC, Observatoire Océanologique, F-66651, Banyuls/mer, France
3
Earth and Ecosystem Sciences, Desert Research Institute, 2215 Raggio Parkway, Reno NV 89512
Marine bacterioplankton diversity was examined at several time points over the annual cycle
at sub-Antarctic Kerguelen Islands (KI) and Antarctic Peninsula (AP) coastal sites in order to establish
a better understanding of the extent and nature of variation at these different latitudes. A combination
of molecular ecological methods targeting the 16S rRNA gene (DGGE, CE-SSCP and massively
parallel v6 tag pyrosequencing) provided increasing degrees of information concerning the richness,
evenness and identity of marine bacterioplankton. The findings suggest that the sub-Antarctic was
more diverse while the extent of temporal variation in the Antarctic Peninsula was higher. The largest
shifts in diversity coincided with phytoplankton blooms arising with the spring or spring to summer
transition in both locations. Deep tag sequencing results corroborated with the DDGE and CE-SSCP
profiling though some differences appeared in the relative abundances (or intensities of peaks or
bands) of sequences detected. Though the KI and AP bacterioplankton communities overall harboured
low similarity levels; the majority of sequenced v6 rRNA gene tags showed a seasonal trend, in which
three times more tags were associated with winter. The distribution of sequences within the
Gammaproteobacteria, Alphaproteobacteria and Bacteriodetes differed between the two regions
studied. Cosmopolitan oceanic bacterioplankton such as SAR11, and the Southern Ocean RCA cluster
varied little with season and were dominant at both sites. A number of abundant Rhodobacteraceae
and uncultivated Gammaproteobacteria-associated tags illustrated intense seasonal variation at both
sites however. This new broadened and deeper understanding of bacterioplankton diversity and
ecology will contribute to an expanding baseline concerning high latitude bacterioplankton that will
serve as an anchor as we move to developing approaches and sensitive indicators to understand
climate change impacts in the polar oceans.
THE ROSEOBACTER RCA CLUSTER – ITS OCCURRENCE, DIVERSITY
AND POTENTIAL
SIGNIFICANCE
GIEBEL H.-A1, D. KALHOEFER1, S. VOGET2, T. BRINKHOFF1 AND M. SIMON1
1
Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg,
26111 Oldenburg, Germany
2
Göttingen Genomics Laboratory, University of Göttingen, Grisebachstr. 8, 37077 Göttingen,
Germany
Clone sequences of the Roseobacter Clade Affiliated (RCA) cluster constitute the largest
cluster within the roseobacters and derive predominantly from planktonic habitats. The aim of our
studies was to quantify its occurrence in the Southern Ocean and the temperate North Sea and to
obtain isolates for further physiological and genomic studies. The biogeographical occurrence of RCA
bacteria was restricted from temperate to polar regions indicating adaptations to colder habitats.
Analyses by RCA-specific quantitative PCR showed that in the Southern Ocean this phylogenetic
narrow lineage constituted up to 36% of total bacterial 16S rRNA genes with highest fractions in the
Antarctic coastal current. In the southern and eastern North Sea RCA bacteria constituted up to 15 and
21% of total bacterial 16S rRNA genes in fall and spring, respectively. Local RCA abundance was
positively correlated to phaeopigments and chlorophyll, dissolved and particulate organic carbon,
turnover rates of dissolved free amino acids, temperature, and negatively to salinity. Three 16S rRNA
RCA phylotypes were detected in total, whereas in most samples only one phylotype was observed.
An abundant RCA strain, “Candidatus Planktomarina temperata”, was isolated from the southern
North Sea by applying dilution cultures. This strain has an identical 16S rRNA gene sequence to the
dominant RCA phylotype detected. The analysis of the closed genome of this isolate of a size of 3.2
Mb and 3042 genes showed the presence of the entire BChl a operon. Our studies show that the RCA
cluster constitutes an abundant group of pelagic Alphaproteobacteria in polar as well as temperate
marine regions and indicate that RCA bacteria play an important role during decaying phytoplankton
blooms. Upcoming genomic analyses and comparisons to other roseobacters accompanied by
investigations of distinct physiological processes will reveal specific adaptations of RCA bacteria to
the pelagic habitat.
PRODUCTION AND OCCURRENCE OF SIDEROPHORES ALONG AMT TRANSECTS
GLEDHILL M.1, E. MAWJI1, A. MILTON1, G. TARRAN2, M. V. ZUBKOV3, G. WOLFF4, A. THOMPSON4,
1
AND E. P. ACHTERBERG
1
School of Ocean and Earth Science, National Oceanography Centre, University of Southampton,
Southampton, SO14 3ZH, UK
2
Plymouth Marine Laboratory, Plymouth, PL1 3DH, UK
3
National Oceanography Centre, Southampton SO14 3ZH, UK
4
Department of Earth and Ocean Sciences, University of Liverpool, Liverpool, L69 3GP, UK
Iron concentrations in the oceans are very low, varying between <0.5 nM in the open ocean to
approximately 20 nM in coastal waters. Iron is known to influence productivity and biodiversity in
many parts of the world’s oceans. A complete understanding of the influence of iron on ocean biology
depends on our knowledge of (1) the processes controlling iron inputs and losses from the surface of
the oceans and the (2) mechanisms governing iron uptake by marine organisms. An important factor
underlying both these issues is the need for a thorough understanding of iron speciation in seawater.
Iron is thought to be predominantly complexed by organic ligands. The nature of these ligands is
currently unknown, however, they have been hypothesized to be produced by biological activity
within the water column. In this presentation we describe investigations into one type of iron complex
produced by marine bacterioplankton – the siderophores. Siderophores are high affinity iron
complexing ligands produced by bacteria as part of their iron uptake mechanism. We describe the
variation in siderophore occurrence and production across the biogeographical regions of Atlantic
Ocean. Siderophore concentrations measured in seawater varied geographically and correlated weakly
with the number of heterotrophic bacteria. We found that siderophores were produced in nutrient
enriched seawater incubations throughout the Atlantic Ocean. The variety and concentration of
siderophores produced in incubations varied with both geographical location and carbon source.
BACTERIAL-ALGAL MUTUALISM AND IRON SUPPLY
GREEN D.1, S. AMIN2, M. HART1, W. SUNDA3, F. KÜPPER1 AND C. CARRANO2
1
Scottish Association for Marine Science, Oban, Scotland, UK
Dept. Chemistry and Biochemistry, San Diego State University, USA
3
Beaufort Laboratory, National Oceanographic and Atmospheric Administration, Beaufort, USA
2
As a part of studies to understand the diversity and functions of bacteria that associate with
dinoflagellates and coccolithophores, we observed one genus of bacteria to be ubiquitous in laboratory
cultures – the Marinobacter. This frequency of algal-bacterial association suggested the existence of a
specific relationship. Abundant siderophore production was observed and viewed as one possible
connection between the two bionts–as iron is often very scarce in the sea. Structural analysis identified
the siderophore to be vibrioferrin (VF), and that the VF-Fe complex was exquisitely sensitive to light,
producing biologically-available Fe(II) as the product photolysis. Using bacterial-free dinoflagellate
cultures supplied with VF-Fe chelates, exposure to light was observed to significantly enhance algal
Fe uptake rates. Genome analysis of one of our VF-producing Marinobacter revealed an unusually
high incidence of eukaryotic-like proteins and the secretion systems, I, II, IV and VI. This coupled
with metabolic data, suggests that this bacterium is tuned to the metabolism of algal metabolites, and
has the genetic apparatus to associate with eukaryotes. We propose that this model represents the
evolution of a mutualistic relationship to solve the perennial problem of algal iron supply in exchange
for a good place to live.
ACTIVELY REPLICATING BACTERIA IN THE MID-ATLANTIC BIGHT AND SARGASSO SEA
GRIM S., B. J. CAMPBELL AND D. L. KIRCHMAN
School of Marine Science and Policy, University of Delaware, Lewes, DE 19958 USA
Bacteria play an essential role in the fluxes of dissolved organic matter and nutrients in the
marine environment. Bulk bacterial production assays have proven useful for estimating the
contribution of bacteria to carbon fluxes, but these assays cannot resolve the roles of community
diversity and structure in determining overall rates. Indeed, the scope of these assays may miss a "rare
but active" fraction of the bacterial community. Our research goal is to isolate and identify the "rare
but active" fraction through the incorporation of a thymidine analog and compare it to the total and
"inactive" communities. In this study we assessed marine bacterial activity and community shifts in
coastal and open ocean environments through the uptake of 5-bromo-2'-deoxyuridine (BrdU), which
traces DNA synthesis. Samples from the Mid-Atlantic Bight and Sargasso Sea were incubated with
BrdU to label bacterial DNA. Total community DNA was extracted, and the labeled fraction was
immunochemically isolated and analyzed using PCR with universal bacterial PCR primers.
Community profiles of the labeled and unlabeled fractions were obtained with denaturing gradient gel
electrophoresis. Control samples not treated with BrdU were similarly analyzed. An active fraction of
marine bacteria was evident through BrdU labeling, which revealed differences between the labeled
and untreated communities. In addition, community structure and activity as assessed through BrdU
uptake varied between the two sites. Further examination of diversity is underway with 454
pyrosequencing, and evaluations of abundance of active bacterial clades are planned using specific
primers and QPCR. The examination of bacterial activity using BrdU labeling will help evaluate the
ecological roles of active bacteria in the marine environment, and will provide further knowledge of
the interplay between community diversity and activity.
DISTRIBUTION OF C AND N CYCLING IN THE
BIOGEOCHEMICAL RATE MEASUREMENTS
NORTH ATLANTIC: GENE
ABUNDANCE VERSUS
HERNDL G. J.1,2, E. SINTES1 AND K. BERGAUER1
1
Dept. of Marine Biology, Faculty Center of Ecology, University of Vienna, Althanstrasse 14, A-1090
Vienna, Austria
2
Dept. of Biological Oceanography, Royal Netherlands Institute for Sea Research (NIOZ), P.O. Box
59, 1790 AB Den Burg, The Netherlands
The deep-water masses of the North Atlantic undergo substantial alterations from their
formation in the northern regions to the equatorial regions in terms of inorganic nutrient
concentrations and microbial community composition and activity. In the northern North Atlantic,
ammonium concentrations are relatively high, even in the bathypelagic waters, coinciding with the
presence of ammonia oxidizing Archaea with an amoA gene encoding an ammonia monooxygenase
with a putatively lower affinity of ammonia than further south. As all nitrifiers are autotrophs using
carbon dioxide as a carbon source, prokaryotic autotrophy might represent a significant source of
newly fixed organic carbon in the dark ocean. It is estimated that the mesopelagic chemoautotrophic
carbon fixation amounts to about 20-30% of the export phytoplankton production. This ‘dark ocean’s
primary production’, albeit hitherto largely ignored, might stimulate the heterotrophic food web in the
meso- and bathypelagic global ocean. Overall, there is accumulating evidence now from actual rate
measurements and molecular approaches that the dark ocean’s prokaryotic community is, on a per cell
level, more active than assumed hitherto. Buoyant or slowly sinking particles in the dark ocean, not
collected by sediment traps might represent hot-spots of microbial activity leading to a non-random
distribution of microbes. Reconciling the carbon budget for the deep waters of the North Atlantic and
for the global dark ocean in general, remains a major challenge, as the measured meso- and
bathypelagic carbon demand exceeds the supply by about an order of magnitude. Potential pitfalls in
our current understanding of the dark ocean’s carbon flux will be discussed.
SPATIAL PATTERNS OF LIGHT STIMULATED BACTERIAL HETEROTROPHIC
PRODUCTION
JEFFREY W.H.1, J.D. PAKULSKI1, A.J. BALDWIN1, J.P. KASE1, J.A. MOSS1, F. JOUX2,3 AND P.J. NEALE4
1
Center for Environmental Diagnostics and Bioremediation, University of West Florida, Pensacola,
FL, USA
2
UPMC Univ Paris 06, UMR 7621, LOMIC, Observatoire Océanologique, F-66651 Banyuls/mer,
France
3
CNRS, UMR 7621, LOMIC, Observatoire Océanologique, F-66651, Banyuls/mer, France
4
Smithsonian Environmental Research Center, Edgewater, MD, USA
Over the past decade there has been considerable interest in photoheterotrophic
bacterioplankton in the world’s oceans. Most of the interest in these organisms has focused on the
presence of aerobic anoxygenic phototrophs (AAP) and bacteria that contain proteorhodopsins. The
functional role of these organisms in carbon cycles, however, remains largely unknown. During this
same period, we have been conducting extensive studies of the effects of solar radiation on
heterotrophic bacterioplankton production in a wide variety of marine environments. While our
primary goal has been to study the effects of ultraviolet radiation, we have often observed that visible
light stimulates the incorporation of 3H-leucine and 3H-thymidine. While this observation is
widespread, it is not universal. For example, a transect of the Pacific Ocean from 70º N to 68º S
showed distinct regions of light stimulated 3H-leucine incorporation that began by 60º N and increased
through temperate and subtropic waters in both hemispheres before ceasing in temperate waters of the
southern hemisphere. Only at the southern most station (68º S) did we again observe photostimulation
of leucine incorporation. In contrast, stimulation of thymidine incorporation was only observed at
three regions (35º to 43º N; 2º S; 30º S). There were four regions where thymidine incorporation was
inhibited by visible light but only one region where leucine incorporation was inhibited. In subsequent
studies we have observed this process to vary seasonally and by location including samples collected
in the Arctic Ocean, Gulf of Mexico, and the Mediterranean Sea. The dissimilarity observed in the
patterns of the two substrates suggests that unique community structures at the different locations
probably contributed to the observed effects of light
O RGANISMS , GENES, PATHWAYS
AND REGULATION OF DIMETHYL SULFIDE PRODUCTION
FROM DIMETHYLSULFONIOPROPIONATE – A SURFEIT OF BIODIVERSITY
JOHNSTON A.W.B., J.D. TODD, A.R.J. CURSON, M.J. SULLIVAN AND M. KIRKWOOD
School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, U.K.
Different marine bacteria are known to catabolise the abundant anti-stress compound
dimethylsulfoniopropionate (DMSP), which is made by many marine plankton and a few land plants.
Some of these pathways liberate dimethyl sulfide (DMS) an environmentally important volatile that is
involved in the global sulfur cycle, in the induction of cloud cover over the oceans and which is a
chemoattractant for many marine animals.
We study the ddd genes in different bacteria, which allow them to make DMS from DMSP. The main
outcomes of this work are:
(a) We identified five wholly different enzymes that can cleave DMSP into DMS plus other
catabolites (acrylate in some cases, 3-OH-propionate in others).
(b) Several of these enzymes were previously in Domains of Unknown Function and even those with
homologues with known enzymatic function were unexpected.
(c) The ddd genes are subject to horizontal gene transfer, extending to some distantly related
“terrestrial” bacteria and even to some eukaryotic microbes.
(d) Some individual bacterial strains, mainly in the Roseobacter group, have multiple ways to
catabolise DMSP. For example, Roseovarius nubinhibens not only has three DMSP lyases, but it
also contains dmdA, a gene identified by Moran’s group, which encodes a DMSP demethylase.
This is globally important in DMSP catabolism but it does not liberate DMS.
(e) Regulation of the ddd genes has unusual characteristics; (a) in several cases, a DMSP catabolite is
the co-inducer and (b) in one case, the ddd operon has no leader sequence and no Shine-Dalgarno
sequence.
(f) In different bacteria that can fully degrade DMSP, and use it as sole carbon source, the pathways
have similarities, but there are also significant differences in the ancillary ddd genes that encode
steps in the “downstream” catabolic steps.
The relative importance of these pathways in the sulfur cycle will be discussed.
COMMUNITY STRUCTURE AND FUNCTION OF HETEROTROPHIC BACTERIA IN THE OCEANIC
CARBON CYCLE
KIRCHMAN D.L.
School of Marine Science and Policy, University of Delaware, Lewes, DE 19958 USA
One of the most important findings in the earth sciences was the high abundance and activity
of bacteria, indicating that these microbes are key players in the oceanic carbon cycle. Another
important finding was about the high diversity of bacteria in the oceans. This presentation will discuss
the links between these two findings and will address questions about the value of community
structure data in understanding the role of bacteria in processing dissolved organic material (DOM) in
the oceans. It can be argued that we should know as much as possible about the diversity and
community structure of the most abundant organism in the biosphere (bacteria). However, a stronger
argument is that community structure data provide insights into the regulation of DOM mineralization
and the role of bacteria in the carbon cycle of the oceans.
HOW FAST DO MARINE BACTERIA GROW ?
KOBLÍZEK M.1, O. PRÁSIL1 AND B.A.S. VAN MOOY2
1
2
Institute of Microbiology CAS, 379 81 Trebon, Czech Republic
Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
Current data based on radiolabelled Leucine or Thymidine incorporation suggest that marine
bacterioplankton in the oligotrophic upper ocean grows at rates of on division per week. However,
such low rates conflict with observations from laboratory cultures, genomics studies and the role of the
microbial loop in the sea. We analyzed diel changes in bacteriochlorophyll to assess in situ turnover
rates of aerobic anoxygenic phototrophs in the euphotic zone of major oceanic gyres in the Atlantic
and Pacific Oceans. Using this approach we found that phototrophic bacteria in the Sargasso Sea, in
the South Atlantic and in oligotrophic regions of the South Pacific grew at rates of about one division
per day. In addition, bacterial phospholipid biosynthesis rates showed similar turnover rates for the
broader bacterioplankton community. These results indicate that the bacterioplankton community in
the upper oligotrophic oceans grows at rates of about one division per day, which is almost an order of
magnitude faster than current estimates. This suggests that bacteria and microbial loop play much
more important role in the marine carbon cycle than currently appreciated.
IMPACT OF SAHARAN DUST DEPOSITION ON THE BACTERIAL DIVERSITY AND ACTIVITY IN
THE NW MEDITERRANEAN SEA
LAGHDASS M.1,2, S. BLAIN1,2, M. BESSELING1,2, P. CATALA1,2, C. GUIEU 3,4 AND I. OBERNOSTERER1,2
1
UPMC Univ Paris 06, UMR 7621, LOMIC, Observatoire Océanologique, F-66651 Banyuls/mer,
France
2
CNRS, UMR 7621, LOMIC, Observatoire Océanologique, F-66651, Banyuls/mer, France
3
Laboratoire d’Océanographie de Villefranche/Mer, CNRS-INSU UMR7093, Observatoire
Océanologique, F-06230, Villefranche-sur-Mer, France
4
Université Pierre et Marie Curie-Paris 6, UMR 7093, LOV, Observatoire Océanologique, F-06230,
Villefranche-sur-Mer, France
The biogeochemical response of the oligotrophic marine environment to dust deposition is
likely in part driven by heterotrophic bacteria as they benefit from the input of new nutrients, and they
also mediate important biogeochemical processes like changes in iron bioavailability. In this context,
the impact of Saharan dust deposition on the bacterial community composition was investigated in 6
large mesocosms (52 m3) deployed at an oligotrophic coastal site in the NW Mediterranean Sea in
June 2008 (project DUNE). Applying the fingerprinting technique CE-SSCP, we observed a temporal
evolution over the 8 days experimental period of the total (16S rRNA gene) and active (16S rRNA
transcripts) bacterial community in both the free-living (< 0.8µm) and particle attached (> 0.8 µm)
size fractions. A response to dust addition was detectable only in the composition of the active
attached bacterial community at the end of the experiment. 16S rRNA gene clone libraries and CARDFISH revealed that the two OTUs Thiothrix and Alteromonas belonging to Gammaproteobacteria and
the Bacteroidetes OTU NS5 were specific to or more abundant in the dust amended than the control
mesocosms, however, with overall low relative abundances. Combining our results from the clone
libraries and CE-SSCP indicated that dust addition enhanced the relative contribution of Alteromonas
macleodii to the active bacterial community attached to particles. The impact of Saharan dust on the
activity of particle-attached bacteria suggests a link to the amount and the composition of particles
present after dust addition.
TEMPERATURE EFFECTS ON VARIATION OF COMMUNITY RESPIRATION
LAI C.-C.1 AND F.-K. SHIAH2
1
Institute of Oceanography, National Taiwan University, Taiwan
Research Center for Environmental Change, Academia Sinica, National Taiwan University, National
Taiwan Ocean University, Taiwan
2
With a two-years (May, 2006~ April 2008) weekly data set take from a P-limited reservoir,
this study tried to explore the potential mechanisms in controlling the temporal variation of
community respiration rate (CR, 1.18~16.99 mMO2 d-1), bacterial respiration (BR, 0.13~13.03 mMO2
d-1) and the relative importance of BR to CR. The results showed that CR, BR, and dissolve organic
carbon (DOC, 38.94~301.63 mMC) were all positively correlated with temperature; while total
nitrogen (NO2+NO3, 9.54~73.72 mMN) showed a negative trend with temperature. Laboratory
temperature manipulation experiments revealed that temperature could affect CR and BR directly.
These indicated that temperature might be the major controlling factor for CR and BR. As to BR
contribution, the BR/CR ratio ranged from 3.9~98.8 %, there was no clear seasonal trend of this ratio.
DISTRIBUTION AND EXPRESSION OF SAR11 PROTEORHODOPSINS
LAMI R.1,2,3, N.J. WEST2,4, P. LEBARON2,3 AND D.L. KIRCHMAN1
1
School of Marine Science and Policy, University of Delaware, Lewes 19958, USA
UPMC Univ Paris 06, UMR 7621, LOMIC, UMS 2348, Observatoire Océanologique, F-66651
Banyuls/mer, France
3
CNRS, UMR 7621, LOMIC, Observatoire Océanologique, F-66651, Banyuls/mer, France
4
CNRS, UMS 2348, Observatoire Océanologique, F-66651, Banyuls/mer, France
2
SAR11 is a major phylogenetic group in marine environment and harbors proteorhodopsin (PR),
a transmembrane light-dependant proton pump. In this study, we first examined the distribution of
SAR11-PR by combining quantitative PCR and a browsing of SAR11-PR sequences from the global
ocean sampling dataset and our clone libraries. We found a wide distribution of SAR11-PR cells, but
also the existence of coastal and off-shore PR-SAR11 populations at a low phylogenetic level. In
addition, we examined how PR expression in SAR11 varies over time in Delaware coastal waters during
three 24 h cruises. Expression of SAR11 PR was higher during the day than at night while no
differences were found for 16S rRNA genes. Collectively, these data reinforce the importance of PR in
the distribution and physiology of SAR11 bacteria.
BACTERIAL ASSEMBLAGE COMPOSITION IN THE NORTH ATLANTIC OCEAN REVEALED BY
MASSIVELY PARALLEL SEQUENCING
LAMY D.1,2, H. AGOGUÉ1,3, P. R. NEAL4, M. L. SOGIN4 AND G. J. HERNDL1,2
1
Dept. of Biological Oceanography, Royal Netherlands Institute for Sea Research (NIOZ), P.O. Box
59, 1790AB Den Burg The Netherlands
2
Dept. of Marine Biology, University of Vienna, Althanstraße 14, A-1090 Vienna, Austria
3
Institut du Littoral et de l’Environnement, UMR LIENSs 6250, CNRS-Université de la Rochelle, 2
rue Olympes de Gouges, 17000 La Rochelle, France
4
Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological
Laboratory, 7 MBL Street, Woods Hole, Massachusetts 02543, USA
Bacterial assemblages from subsurface (100 m depth), meso- (200-1000 m depth) and bathypelagic (below 1000 m depth) zones at 10 stations along a North Atlantic Ocean transect from 60°N to
5°S were characterized using massively parallel pyrotag sequencing of the V6 region of the 16S rRNA
gene (V6 pyrotags). In a dataset of more than 830,000 V6 pyrotags we identified 10738 OTUs of
which 52 % were singletons. The singletons accounted for less than 2% of the pyrotag abundance,
while the 100 and 1,000 most abundant OTUs represented more than 76% and 95%, respectively, of
all recovered OTUs. Non-metric Multi-Dimensional Scaling and Canonical Correspondence Analysis
of all the OTUs excluding the singletons revealed a clear clustering of the bacterial communities
according to the water masses. More than 80% of the 1,000 most abundant OTUs corresponded to
Proteobacteria of which 55% were Alphaproteobacteria, mostly composed of the SAR11 cluster.
Gammaproteobacteria increased with depth and included a relatively large number of OTUs for
Pseudomonadales and Alteromonadales. The bathypelagic zone showed higher taxonomic evenness
than the overlying waters, albeit bacterial diversity was remarkably variable. The low-abundance
OTUs were responsible for the distinct bacterial communities characterizing the major deep-water
masses. Taken together, our results reveal that deep water masses act as bio-oceanographic islands for
bacterioplankton leading to water mass-specific bacterial communities in the deep waters of the
Atlantic.
BIOAVAILABILITY OF DISSOLVED ORGANIC MATTER AND BACTERIAL DIVERSITY: INSIGHTS
FROM CHEMOSTAT CULTURE EXPERIMENTS
LANDA M., BLAIN, S., BATAILLER N., CAPARROS J., CATALA P., DEVEZ, A., LAGHDASS, M. ORIOL,
L. AND I. OBERNOSTERER
UPMC Univ Paris 06, UMR 7621, LOMIC, Observatoire Océanologique, F-66651 Banyuls/mer,
France
CNRS, UMR 7621, LOMIC, Observatoire Océanologique, F-66651, Banyuls/mer, France
The biological availability of marine dissolved organic carbon (DOC) to heterotrophic bacteria
is tightly linked to its source and diagenetic age. Whether different sources of marine DOC are
processed by specific populations of heterotrophic bacteria is presently an unresolved question. We
wanted to test the hypothesis that DOC produced by different phytoplankton species shapes the
composition of the heterotrophic bacterial community through the selection of metabolically adapted
bacterial groups. To address this issue, we used chemostat cultures and studied the response of a
natural community of heterotrophic bacteria to DOC originating from cultures of Phaeodactylum spp.
or Synechococcus spp., respectively. Carbon was the limiting factor throughout the experimental
duration, and the heterotrophic bacterial community was continuously supplied with 15 µM of the
respective source of phytoplankton-derived DOC. The chemostat cultures (6 liters each) were run for
five generation times. We will present first results on bulk parameters such as biomass production and
enzymatic activities of the bacterial communities growing on different sources of DOC. Applying the
fingerprinting method CE-SSCP, we will present results on the impact of DOC sources on the
presence and activity of operational taxonomic units, and discuss the temporal pattern that could
reflect an adaptation of the bacterial community facing different sources of DOC.
SEASONAL SUCCESSION OF PHYTOPLANKTON COMPOSITION IN FEI-TSUI RESERVOIR
LIN C.-H.1, F.-K. SHIAH2 AND T.-Y. HO3
1
Research Center for Environmental Changes, Academia Sinica, National Taiwan University, Taiwan
Research Center for Environmental Change, Academia Sinica, National Taiwan University, National
Taiwan Ocean University, Taiwan
3
Research Center for Environmental Change, Academia Sinica, Taiwan
2
To understand the annual variation of phytoplankton community composition as well as the
relative importance of different phyla in oligotrophic freshwater ecosystem, pigment analysis via
HPLC method was conducted on a weekly basis in the Fei-Tsui reservoir from Oct 2007 to Dec 2008.
Epilimnion (20 m deep) integrated averaged chlorophyll a concentrations (IChl) ranged 0.51~5.55 mg
Chl m-3 with a bloom occurring in autumn. Overall, crytophytes, cyanobateria and diatoms were the
three most dominant phyla accounting for 25, 24 and 20% of total IChl, respectively. Green algae
(chlorophytes and prasinophytes, 12%) and dinoflagellates (10%) ranked the 4th and 5th in term of
relative contribution. The analysis between phyla and environmental factors including temperature,
light and mixed layer depth (a proxy of nutrient supply) was performed to understand potential
controlling mechanisms. Cyanobacteria biomass did not change much during the studied period.
Cryptophytes, prasinophytes and chlorophytes prevailed in the cold, low light level and high nutrient
supply seasons. On the other hand, dinoflagellates could be categorized as warm water and low
nutrient required species. Diatom biomass showed no significant relationships with environmental
factors. It is notable that depletion of diatom bloom in turn was replaced by growing dinoflagellates in
warm season. Furthermore, dinoflagellates occupied the light-rich surface waters in comparison with
diatoms of similar size. Manipulation experiments suggested that plentiful nutrient stimulated the
growth of dinoflagellate more than that of diatoms in high light level and phosphorus-enrichment
conditions. Additionally, we found that zeaxanthin pigment concentrations showed a good correlation
with cyanobacteria abundance with a slope of 1.06 ± 0.04 fg cell-1, which can be used empirically in
converting diagnostic pigment concentrations to cyanobacteria abundance in the study area.
DIFFERENT SALINITIES INFLUENCE MICROBIAL
EVOLUTION IN COASTAL ANTARCTIC LAKES
COMMUNITY COMPOSITION AND
LOGARES R.1,2, E. LINDSTRÖM1, S. LANGENHEDER1, J. LAYBOURN-PARRY3, L. TRANVIK1, S.
BERTILSSON1 AND K. RENGEFORS4
1
Limnology/Dept. of Ecology & Evolution, Uppsala University, Uppsala, Sweden
Institut de Ciències del Mar (ICM), CSIC, Barcelona, Spain
3
Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol, UK
4
Limnology/Dept. of Biology, Lund University, Lund, Sweden
2
Mounting evidence indicates that salt concentration affects the evolution and composition of
aquatic microbial communities. To advance our understanding in this subject, we have studied the
microbial communities inhabiting a group of coastal Antarctic lakes that range from freshwater (0) to
hypersaline (>250) using Sanger/454 rDNA sequencing and experiments. Most of these lakes are
marine-derived closed basins, containing microbial communities that were exposed to drastic salinity
changes since the formation of the lakes (<10,000 years). Other lakes are freshwater and were formed
by melt-water from the Antarctic ice-plateau. Our results indicated that long-term salinity shifts had a
strong influence on the richness, evenness and possibly evolution of the microbial communities living
in marine-derived lakes. In particular, diversity decreased at salinity extremes (i.e. freshwater or
hypersaline lakes) suggesting strong environmental filtering and local extinctions. Marine-derived
microbes were present in saline lakes, but their richness and evenness differed from ancestral marinecoastal communities. In particular, lakes that became hypersaline appeared to be exclusively
dominated by Archaea. Experimental results indicated that ancestrally marine dinoflagellate
populations have adapted to diverse lake salinities, suggesting that adaptive evolution may have
played an important role in shaping the present microbial communities in the lakes. Typical freshwater
bacteria were predominant in freshwater lakes, instead of marine-derived groups adapted to low
salinity. Freshwater bacteria clustered phylogenetically with lineages present in ice (European glaciers
and perennial ice cover of distant Antarctic lakes) and north temperate lakes, suggesting intra- and
intercontinental colonisations. Altogether, our results contribute to understand how microbial
communities react to environmental change and give insight on microbial long-range colonization
capabilities.
EFFECTS OF PHOSPHORUS LIMITATION ON MARINE NATURAL PHYTOPLANKTON
COMMUNITY STRUCTURE AND FUNCTION
LY J.1, J. KROMKAMP1 AND K.C. TIMMERMANS2
1
Netherlands Institute of Ecology (NIOO-KNAW), Centre for Estuarine and Marine Ecology, P.O.
Box 140, 4400 AC Yerseke, The Netherlands
2
Royal Netherlands Institute for Sea Research (NIOZ), P.O. Box 59, 1790 AB Den Burg, Texel, The
Netherlands
It is currently under debate whether nitrogen, phosphorus or both regulated the primary
producers in the marine environment. Phosphorus has been recently considered as a limiting and
important nutrient for phytoplankton in coastal ecosystems; however it remains much less documented
though no less important. In long term surveys, the Dutch Wadden Sea has been characterized as
changing systems; especially a decline of phosphorus had been shown in this systems. The question
remains whether the potential P limitation has an impact on phytoplankton community structure and
function. A series of nutrient enrichment experiments have been conducted in spring period with
addition of different source of nutrients. For each sampling time, fundamental controls of primary
production and phytoplankton community composition are measured such as phytoplankton biomass
and photosynthesis activity (maximum quantum yield of photosystems II Fv/Fm and rapid light curves).
In addition, specific primary production using stable isotope 13C incorporated into phospholipids fatty
acids (PLFA) has been measured to assess photosynthetically active organisms in the water mass and
alkaline phosphatase activity, use as a common enzyme indicator of phosphorus deficiency in
phytoplankton has been quantified via the molecular probe ELF®. We are currently analyzing these
environment samples which will allow us to examine how the phytoplankton community changes
under a reduction of phosphorus nutrient in the water. Additionally, we are currently looking for
eukaryotic microalgae genes which are involved in phosphorus limitation. This might reveal an
unexpected ecological role in biogeochemistry cycling.
DYNAMIC BACTERIAL
COMMUNITIES ON REVERSE-OSMOSIS MEMBRANES IN A FULL-SCALE
DESALINATION PLANT
MANES DE O. C-L.1,2, N.J. WEST1,3, S. RAPENNE4 AND P. LEBARON1,2
1
UPMC Univ Paris 06, UMR 7621, LOMIC, UMS 2348, Observatoire Océanologique, F-66651
Banyuls/mer, France
2
CNRS, UMR 7621, LOMIC, Observatoire Océanologique, F-66651, Banyuls/mer, France
3
CNRS, UMS 2348, Observatoire Océanologique, F-66651, Banyuls/mer, France
4
Veolia Environnement - Centre de recherche sur l'eau, Chemin de la Digue 78600 Maisons Laffitte,
France
We studied bacterial community structure and dynamics in different compartments of a fullscale desalination plant. Genetic fingerprinting and 16S rRNA gene clone libraries analysis revealed
that the bacterial community present on sea-water reverse osmosis (SWRO) membranes was very
different from those present in the inflow water, suggesting that specific bacterial groups were adapted
for SWRO membrane colonization. Moreover, there were striking differences in the bacterial
community composition of membranes between different sampling times, whereas the communities
from different water samples taken at different compartments were similar to each other and relatively
stable over time. Alphaproteobacteria and Gammaproteobacteria dominated the water clone libraries,
whereas Betaproteobacteria and Planctomyces were nearly exclusively found in the membrane
libraries. The clustering of sequences at the 97% OTU level revealed that five OTUs were unique to
the membrane used for the shortest period comprising one Betaproteobacteria genus, Ideonella, and
three different Bacteroidetes OTUs. Interestingly, the typical freshwater genus Ideonella was the
dominant OTU for this membrane but was absent from those in use for longer periods. This result
suggests that bacteria affiliated to the Ideonella genus could be one of the SWRO membrane primary
colonizers.
AMMONIUM AND NITRITE OXIDATION (DE) COUPLING IN THE EUPHOTIC ZONE
MOLINA V.1, C. FERNANDEZ2,3,4 AND L. FARIAS1,4
1
Laboratorio de Procesos Oceanográficos Física y Clima, Universidad de Concepción, Casilla 160-C,
Concepción, Chile
2
UPMC Univ Paris 06, UMR 7621, LOMIC, Observatoire Océanologique, F-66651 Banyuls/mer,
France
3
CNRS, UMR 7621, LOMIC, Observatoire Océanologique, F-66651, Banyuls/mer, France
4
Centro de Investigación Oceanográfica en el Pacífico Sur-Oriental (FONDAP-COPAS), Universidad
de Concepción, Casilla 160-C, Concepción, Chile
The coastal area of central Chile (36°S) is characterized by the influence of seasonal winddriven upwelling of low-oxygen (<22 mM), nutrient-rich waters that fertilize the euphotic zone,
enhancing primary productivity. Intense degradation of recently produced organic matter at depth also
results in significant ammonium availability for nitrifying assemblages. We explored the variability of
ammonium oxidation by b-Proteobacteria (bAOB) and archaea (AOA) as well as the coupling of
ammonium and nitrite oxidation during active and non active upwelling conditions. AOA and bAOB
were studied by the ammonia monooxygenase subunit A (amoA) genes to explore their diversity while
their abundance was approached through Q-PCR in DNA and cDNA. Parallel biogeochemical
measurements using stable isotopes (15N) and specific Amo and archaeal inhibitors allowed studying
the interaction among the ammonium and nitrite oxidizing communities.
Measurements of total nitrification showed active nitrate production during the upwelling
season with average daily rates of 41 ± 23 nM d-1. Nitrite oxidation was also estimated and reached
rates equivalent to those of ammonium oxidation, suggesting a tight coupling between both phases of
the nitrification process within the oxygen deficient layer. A single lineage of bAOB, Nitrosospira
spp, was present in the water column during the upwelling season, whereas AOA showed a higher
diversity that was distributed in all known planktonic clusters. AOA and bAOB average abundances
were higher during the upwelling season with values of 15,04 and 167 amoA copies/ml, respectively,
than during non-upwelling season (5,91 and 61 amoA copies/ml, respectively). AOA abundance in
cDNA also suggests that AOA contribute greatly to aerobic ammonium oxidation mainly during the
upwelling season. In summary, our results suggest that ammonium oxidation can be a significant
process in seasonal upwelling areas and is performed by an assemblage of archaea and bacteria with
changing contribution along the seasonal cycle.
EMERGING HORIZONS IN BIODIVERSITY AND ECOSYSTEM FUNCTIONING RESEARCH
MONTOYA J.
Marine Sciences Institute (ICM-CSIC), Barcelona, Spain
Two decades of intensive research have provided compelling evidence for a link between
biodiversity and ecosystem functioning (B-EF). Whereas early B-EF research concentrated on species
richness and single processes, recent studies have investigated different measures of both biodiversity
and ecosystem functioning, such as functional diversity and joint metrics of multiple processes. There
is also a shift from viewing assemblages in terms of their contribution to particular processes toward
placing them within a wider food web context. I will present how biodiversity effects are shaped by
multitrophic interactions. Further, I discuss how B-EF metrics and food web relations could be
addressed simultaneously. I conclude that addressing traits, multiple processes and food web
interactions is needed to capture the mechanisms that underlie B-EF relations in natural assemblages.
Finally, I will discuss whether these new horizons may be relevant and practical to address
relationships between biodiversity and ecosystem functioning in microbial communities.
A BIOGEOCHEMIST' S G UIDE
ANALYSIS
TO
Q UANTITATIVE C OMPARATIVE METATRANSCRIPTOME
MORAN M. A., S. GIFFORD, S. SHARMA AND J. RINTA-KANTO
University of Georgia, Athens GA 30602 USA
The potential of metatranscriptomic sequencing to provide insights into the environmental
factors that regulate microbial activities depends on how fully the sequence libraries capture
community expression (i.e., sample sequencing depth and coverage depth), and the sensitivity with
which expression differences between communities can be detected (i.e., statistical power for
comparative analysis). We will discuss approaches for making metatranscriptomic data sets more
quantitative and comparative. Addition of an internal standard during RNA extraction provided a way
to calculate absolute transcript numbers. Coastal waters of the southeastern U.S. were determined to
contain 1 x 1012 bacterioplankton mRNA molecules per liter of seawater, although each bacterium
averaged only ~190 mRNA molecules per cell. Even large bacterioplankton metatranscriptomic
libraries containing ~500,000 possible protein-encoding sequences had low sample sequencing depth,
with <1 out of every 10 million mRNA molecules sequenced. The internal standard also allowed
quantitative (per liter) estimates of mRNAs representing diagnostic genes marine elemental cycles,
providing absolute benchmarks against which time-series and experimentally manipulated
transcriptomes can be compared. However, many biogeochemically informative transcript categories
had too few counts for robust statistical hypothesis testing, even in large metatranscriptomic libraries.
Representing microbial genes and transcripts in a quantitative framework provides an essential bridge
between "omics" data and the larger scale ocean processes captured in biogeochemical measures and
ecosystem models.
THE SEASONAL VARIATION OF IRON STRESS IN THE SCOTIA SEA
NIELSDOTTIR M. C.1, T. S. BIBBY1, C. M. MOORE1, R. SANDERS1, D. J. HINZ1, R. KORB2, M.
WHITEHOUSE2 AND E. P. ACHTERBERG1
1
School of Ocean and Earth Science, National Oceanography Centre, Southampton, University of
Southampton, European Way, Southampton, SO14 3ZH, UK
2
British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
Large phytoplankton blooms are associated with islands and shallow water regions in the
otherwise low biomass Southern Ocean. The seasonal phytoplankton bloom associated with South
Georgia in the Scotia Sea is the largest in the Southern Ocean and displays the greatest longevity, with
a clear enhanced signal in satellite derived chlorophyll for a duration of ~16-20 weeks. The work
presented here is the first comprehensive study of seasonal variations in phytoplankton biomass and
iron availability in the Scotia Sea for the austral spring and summer seasons. The Scotia Sea to south
of the islands of South Georgia exhibited low dissolved iron (dFe) surface water concentrations
(<0.01-0.05 nM) and low Fv/Fm values (indicative of iron stress) during the spring and summer
seasons. Nevertheless, chlorophyll a concentrations of up to 1.4 mg m-3 indicated a sufficient iron
supply possibly from the Antarctic mainland and winter overturning to initiate bloom conditions.
Surface water concentrations of dissolved iron (dFe) in the South Georgia bloom waters (north of the
islands) were slightly higher during summer than spring (0.31 nM compared to 0.20 nM, with P>0.05)
and the nitrate drawdown between the two seasons was 16 uM nitrate, indicative of new production.
We suggest that the South Georgia bloom is sustained by a continuous benthic supply of iron from the
South Georgia shelf. In addition, enhanced dFe concentrations (ca. 0.25 nM) were observed in a
cryptophyte dominated bloom in the southern Scotia Sea near the South Orkney Islands, which
highlights important differences in phytoplankton bloom dynamics for the Southern Ocean island
systems.
ECOLOGICAL ROLES OF PROTEORHODOPSIN PHOTOTROPHY IN MARINE BACTERIA
PINHASSI J.
Marine Microbiology, School of Natural Sciences, Linnaeus University, 9182 Kalmar, Sweden
Since the discovery of heterotrophic bacteria being both numerous and actively growing in the
sea, three decades of intense studies have revealed bulk activities and the biodiversity of
bacterioplankton. This has led to the conclusion that marine microbes play a crucial role in regulating
global biogeochemical cycles for many elements. Still, important challenges lay ahead in defining the
role of specific microbial populations in the turnover of particular elements and the fluxes of energy in
the water column. Confounding the picture even more is the surprisingly frequent discovery of novel
metabolisms found among marine microbes, so that the once so easy-to-define division of
microorganisms into heterotrophic and autotrophic compartments no longer seems to hold through.
Just consider the cases of anammox, deep-sea dark carbon dioxide fixation and proteorhodopsin. In the
case of proteorhodopsin, this photoprotein found in representatives of the most diverse groups of longconsidered typically heterotrophic bacteria makes the whole concept of heterotrophy somewhat
diffuse. To what degree are heterotrophic bacteria containing proteorhodopsin really heterotrophic?
Does proteorhodopsin make any difference to the organisms? And in that case, what difference does it
make? And of particular interest to the present workshop, does proteorhodopsin phototrophy have an
impact on the rates of microbially dominated biogeochemical cycling? Although few answers to these
questions are obvious at this time, these issues will be touched upon in this lecture, with examples
from some different proteorhodopsin-containing bacteria.
THE ROLE OF FAECAL PELLET MICRO-ENVIRONMENTS
IN OCEANIC METHANE
PRODUCTION
ROWAN A.K.1, S.T. WILSON2, M.C. HART1, D. H. GREEN1 AND A. D. HATTON1
1
The Scottish Association for Marine Science, Dunstaffnage marine laboratory, Oban, Argyll, PA37
1QA
2
Center for Microbial Oceanography: Research and Education (C-MORE), 1000 Pope Road, MSB 629
Honolulu, HI 96822 USA
Zooplankton faecal pellets in the pelagic environment represent important hotspots for
biogeochemical cycling. Despite this, the microbial communities and processes involved are not well
understood. The ‘oceanic methane paradox’ signifies an example of this. Methane exists at supersaturated concentrations in oxygenated upper oceans and is thought to result from in situ production.
This is paradoxical as methanogens, the organisms thought to be responsible, are considered to be
strict anaerobes. One possible explanation is that anaerobic micro-sites may exist; such as within
zooplankton faecal pellets which may support methanogenic populations. Active methanogensis has
been observed in faecal pellets however there is some debate as to the existence of true anoxic zones,
capable of supporting methanogens, in pelagic particulate material.
We applied culture-independent approaches to determine the microbial communities present in
faecal pellets (Loch Creran, Scotland). Results show that faecal pellets harbour a highly diverse
microbial consortium including methanogens, sulphate-reducers. Furthermore faecal pellet anaerobic
incubations demonstrated methane production and indicated viability of the methanogenic
populations. These findings have important implications for the understanding of microbial
biogeochemical cycling in the pelagic environment.
D IATOM FLUX ASSEMBLAGES FROM A NATURALLY IRON FERTILIZED
IMPLICATIONS FOR CARBON CYCLING IN THE PRESENT DAY AND GLACIAL OCEAN
BLOOM:
SALTER I.1,2,3, R.S. LAMPITT1, A.E.S. KEMP1, G.A. WOLFF4, C. M. MOORE1, J. HOLTVOETH4, M.T.
HERNANDEZ-SANCHEZ5
1
National Oceanography Centre, Southampton, University of Southampton Waterfront Campus,
European Way, Southampton, SO14 3ZH, United Kingdom.
2
UPMC Univ Paris 06, UMR 7621, LOMIC, Observatoire Océanologique, F-66651 Banyuls/mer,
France
3
CNRS, UMR 7621, LOMIC, Observatoire Océanologique, F-66651, Banyuls/mer, France
4
Department of Earth and Ocean Sciences, University of Liverpool, 4, Brownlow Street, Liverpool,
L69 3GP, United Kingdom
5
Department of Chemistry, University of Bristol, Bristol, BS8 1TS, United Kingdom
Changes in the supply of iron to high nutrient low chlorophyll (HNLC) regions are thought to
critically influence marine primary production and export of organic carbon (OC) from the upper
ocean and hence concentrations of atmospheric carbon dioxide in both present day and glacial
scenarios. Purposeful additions have unequivocally demonstrated increased phytoplankton
productivity in response to iron, and naturally Fe-fertilized island systems indicate a concomitant
increase in OC flux. We present data on diatom assemblages and the biochemical properties of sinking
particles to elucidate the mechanisms responsible for enhanced deep-water OC flux in response to
natural iron fertilization (CROZeX) of the Southern Ocean. Our data indicate that the availability of
iron drives segregated adaptations to ecological niches which are reflected in the diatom flux
assemblages and elemental stoichiometry of sinking particles. Deep-water carbon flux from the
naturally-fertilized bloom area is tightly correlated with the resting stage flux of a single diatom
species, Eucampia antarctica. The results suggest that the enhanced carbon flux observed in naturally
fertilized systems is not entirely attributable to iron relief of open ocean diatoms. Instead we suggest
that the advection of neritic centric diatom assemblages from island systems and the subsequent flux
of resting stages significantly contribute to carbon sequestration resulting from natural iron
fertilization. Our data therefore suggest that carbon export estimates from current natural iron
fertilization studies represents a highly specific response of island systems chosen as natural
laboratories. In combination with observations of enhanced nitrate utilization and dominance of E.
antarctica in Last Glacial Maximum sediments our data also suggest a potential role for Eucampia
resting stage ecology in glacial-interglacial CO2 transitions.
SPECIFIC PHYTOPLANCTON – BACTERIA INTERACTIONS THROUGH DISSOLVED ORGANIC
CARBON
SARMENTO H. AND J. M. GASOL
Institut de Ciències del Mar, ICM-CSIC, E-08003 Barcelona, Catalunya, Spain
Marine phytoplankton and heterotrophic prokaryotes (HP) are major components of our
biosphere that interact continuously: HP utilizes the dissolved organic carbon derived from
phytoplankton excretion or cell lysis, and mineralization by HP provides inorganic nutrients for
phytoplankton. For this reason, these two communities are expected to be closely linked, but the fact is
that the two compartments interact in very complex ways that remain largely unexplored. We
developed the use of radiolabeled algal exudates as a tracer in the MAR-FISH technique
(microautoradiography combined with fluorescent in situ hybridization) to quantify the strength of the
interactions between several phytoplankton species and the major phylogenetic groups of HP. The
incubations of sea water with radiolabeled exudates from different algal species revealed major
differences in the percentage of cells of each bacterial type taking up the products. The patterns of the
interactions revealed specific linkages between HP phylogenetic groups and phytoplankton species,
showing that HP community structure can be shaped by the phytoplankton assemblage. Moreover, this
study provided additional information about the intrinsic ecology of each bacterial group: Gammaproteobacteria (particularly Alteromonas) and Roseobacter (Alpha-proteobacteria) increased
remarkably their contribution to total community in terms of biomass when incubated with algal
exudates in a 24h period, while members of Bacteroidetes were very active in the uptake of the labeled
organic compounds in the short term, disproportionally to the net growth of this group in the long
term. The ecological implications of these results are of great relevance explaining the huge bacterial
diversity observed in the sea.
DRIVERS OF ORGANIC MATTER TURNOVER IN THE SEA – SOME EXAMPLES FROM THE
ROSEOBACTER CLADE
SIMON M., S. HAHNKE, H.-A. GIEBEL, H. OSTERHOLZ AND T. BRINKHOFF
Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, D-26131
Oldenburg, Germany
The Roseobacter clade has been shown to be a prominent component of the bacterioplankton
in marine surface waters, predominantly in temperate to polar regions and in particular in the course of
phytoplankton blooms. Several distinct clusters with typical pelagic representatives have been
identified in which phylotypes and a few isolated strains occur. The genome of several of these strains
has been sequenced. Available metagenomic, metatranscriptomic and genomic data provide most
valuable insights into the metabolic potential and gene expression patterns of these roseobacters.
However, surprisingly little work has been done so far on the physiology of representative model
organisms to better understand growth and interactions with other bacterioplankton components and
with phytoplankton and thus specific biogeochemical roles of these organisms. We obtained several
isolates of Roseobacter clusters typical for the water column from the North Sea and examined growth
and various physiological properties, including substrate spectra and interactions with phytoplankton
algae. Isolates belong to the RCA cluster, the SH6-1 cluster which is most closely related to the
NAC11-6 cluster, and others are affiliated closely to the genera Sulfitobacter, Loktanella and
Oceanibulbus. The results show that the isolates have rather distinct preferences for selected amino
acids, monosaccharides and oligosaccharides, and that they can respond very differently to substrates
released from individual algal species. Some of these observations are in line with the seasonal
occurrence of these strains in the North Sea in the course of phytoplankton blooms and may explain
some aspects of their growth control. The isolates provide a valuable basis for detailed analyses of
specific processes in the organic matter cycling in pelagic systems and complement metagenomic and
metatranscriptomic analyses. They may further be used for systems biology approaches in microbial
oceanography.
ARCHAEAL AMOA: NEW INSIGHTS INTO THE DIVERSITY AND BIOGEOGRAPHY OF ARCHAEAL
AMMONIA OXIDIZERS
SINTES E.1,2, K. BERGAUER1, D. DE CORTE2,3 AND G. H. HERNDL1,2
1
Department of Marine Biology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
Department of Biological Oceanography, Royal Netherlands Institute for Sea Research (NIOZ), PO
Box 59, 1790 AB, Den Burg, The Netherlands,
3
Center for Ecological and Evolutionary Studies, University of Groningen, PO Box 14, 9750 AA
Haren, The Netherlands
2
Mesophilic archaeal ammonia oxidizers (AOA) are abundant in a diverse range of
environments ranging from soils to sediments, and from freshwater to marine systems. The presence
of diverse and distinct crenarchaeal communities in different habitats, as well as a few cosmopolitan
AOA have been described. Results with different primer sets developed for AOA over the last years
revealed remarkable differences in the abundance of AOA in the oceanic realm. In an attempt to
resolve this apparent discrepancy, we used two previously applied archaeal amoA primer sets and
compared them in two contrasting environments, a shallow Arctic and a deep open Atlantic site.
Applying these two archaeal amoA primer sets, we could distinguish an AOA cluster dominating at
the base of the euphotic layer in the Atlantic (100 m) and in the Artic throughout the water column
(down to 300 m) from a deep-water crenarchaeal cluster extending from 250 m to 7000 m in the
Atlantic. Thus, the two different AOA clusters apparently harbor two different amoA genes related to
the prevailing environmental conditions, particularly the ammonia availability. The two different
amoA genes encode amoA proteins with putatively different substrate affinity allowing the two AOA
clusters to occupy different ecological niches resulting in a specific stratification with depth and a
distinct biogeography. Future work to unveil the actual role of the AOA in the nitrogen cycle must
therefore focus on the isolation of these different groups and the characterization of their ammonia
oxidation kinetics.
IN
SITU GENE EXPRESSION BY MARINE BACTERIOPLANKTON AT HIGH PHYLOGENETIC
RESOLUTION
SUZUKI M.T.
1
UPMC Univ Paris 06, UMR 7621, LOMIC, UMS 2348, Observatoire Océanologique, F-66651
Banyuls/mer, France
2
CNRS, UMR 7621, LOMIC, Observatoire Océanologique, F-66651, Banyuls/mer, France
Marine bacterioplankton, and their genomes have been the subjects of major research
initiatives in the past decade and a vast amount of new knowledge has been gathered. This is
particularly true for their spatial and temporal distributions and metabolic capabilities. However
measurements of activity by specific prokaryotes in the environment are still lacking for the full
understanding of their roles in the biogeochemistry of the Ocean. For the past five years we have
worked on measuring the activity on specific bacterioplankton based on messenger RNA
quantification using real time quantitative PCR. The level of phylogenetic resolution to be targeted by
these assays is one issue frequently associated with the approach in environmental settings. We will
present results of two studies where a relatively fine level of resolution (i.e. discrimination of different
DNA sequences, coding nearly-identical amino acid sequences) was chosen. Diel measurements of
SAR11-like proteorhodopsin-coding genes at the Pacific station Aloha and of the cell division gene
ftsZ in a NW Atlantic coastal site showed patterns suggestive of biological responses to the diel cycle,
even though in both cases it appears that different subpopulations (i.e. patches) were sampled due to
advective effects. These studies showcase the feasibility of the gene expression approach, but
emphasize the need for studies comparing gene expression at different levels of phylogenetic
resolution.
FUNCTIONAL DIVERSITY OF BACTERIOPLANKTON ACROSS THE MEDITERRANEAN SEA
ASSESSED BY FLOW CYTOMETRY, CELL SORTING AND FISH TECHNIQUES
TALARMIN A.1, 2, 3, F. VAN WAMBEKE1, P. CATALA2,3, C. COURTIES2,4 AND P. LEBARON2, 3
1
Laboratoire de Microbiologie, Géochimie, & Ecologie Marines, UMR CNRS 6117, Université de la
Méditerranée, Campus de Luminy, F-13288 Marseille, France
2
UPMC Univ Paris 06, UMR 7621, LOMIC, UMS 2348, Observatoire Océanologique, F-66651
Banyuls/mer, France
3
CNRS, UMR 7621, LOMIC, Observatoire Océanologique, F-66651, Banyuls/mer, France
4
CNRS, UMS 2348, Observatoire Océanologique, F-66651, Banyuls/mer, France
Small-sized organisms are major actors of the biogeochemical cycles in poor marine
environments like oligotrophic oceans. Their diversity is being increasingly documented, and so is
their potential role in carbon export from surface to deep ocean. Bacterioplanktonic organisms are
numerous and, as sustainers of primary and heterotrophic production in the Mediterranean Sea, they
also are hard competitors towards depleted resources like nutrients. Competitive abilities impact both
bacterioplanktonic diversity and functionality. Are microorganisms getting adapted to ecological
niches or do they develop physiological strategies to fit in rapid environmental changes? Our study
focuses on the Mediterranean Sea that was investigated from East to West during the BOUM cruise in
summer 2008. The distribution of bacterioplanktonic organisms was examined through flow cytometry
(FCM), more specific groups of heterotrophic prokaryotes were targeted using a fluorescent in situ
hybridization technique, and the heterotrophic activity of specific population was accessible thanks to
a combination of radiolabeling and cell sorting techniques. At a station in the South West of Sardina,
maximum abundances of Prochlorococcus and heterotrophic prokaryotes were met on the whole
transect. The diversity of heterotrophic prokaryotes was not clearly dominated by one but shared
among 3-4 phylogenetic groups. Abundances of FCM-enumerated organisms linked to their cellular
3
H-Leucine incorporation rates showed the contribution of each sorted population to the total
heterotrophic production. The assumed autotrophic nature of cyanobacterial cells was misleading as it
was recently observed on natural samples from the North Atlantic and North Pacific Subtropical
Gyres: at some layers, cyanobacteria contributed up to 50% to the heterotrophic production. Would
mixotrophy be a key to survival in oligotrophic environments?
GROWTH RATES OF DIFFERENT PHYLOGENETIC BACTERIOPLANKTON
GROUPS IN A COASTAL
UPWELLING SYSTEM
TEIRA E.1, S. MARTÍNEZ-GARCÍA1, C. LØNBORG2,3 AND X. A. ÁLVAREZ-SALGADO2
1
Departamento de Ecoloxía e Bioloxía Animal, Universidade de Vigo, 36310 Vigo, Spain
CSIC, Instituto de Investigacións Mariñas, Eduardo Cabello 6, 36208 Vigo, Spain
3
Scottish Association for Marine Science, Oban, Argyll, PA37 1QA, United Kingdom
2
Microbial degradation of dissolved organic matter (DOM) in planktonic ecosystems is carried
out by diverse prokaryotic communities, whose growth rates and patterns of DOM utilization
modulate carbon and nutrient biogeochemical cycles at local and global scales. Nine dilution
experiments (September 2007 to June 2008) were conducted with surface water from the highly
productive coastal upwelling system of the Ría de Vigo (NW Iberian Peninsula) to estimate bacterial
growth rates of six relevant marine bacterial groups: Roseobacter, SAR11, Betaproteobacteria,
Gammaproteobacteria, SAR86 and Bacteroidetes. Surprisingly, SAR11 dominated over the other
bacterial groups in autumn, likely associated to the entry of nutrient-rich, DOC-poor Eastern North
Atlantic Central Water (ENACW) into the embayment. Roseobacter and SAR11 showed significantly
opposing growth characteristics. SAR11 consistently grows at low rates (range 0.19-0.71 d-1), whilst
Roseobacter, has a high growth potential (range 0.70-1.64 d-1). By contrast, Betaproteobacteria,
Bacteroidetes, SAR86 and Gammaproteobacteria growth rates widely varied among experiments.
Regardless of such temporal variability, mean SAR86 growth rate (range 0.1-1.4 d-1) was significantly
lower than that of Gammaproteobacteria (range 0.3-2.1 d-1). Whereas the relative abundance of
different bacterial groups showed strong correlations with several environmental variables, groupspecific bacterial growth rates did not covary with ambient conditions. Our results suggest that
different bacterial groups exhibit characteristic growth rates, and, consequently, distinct competitive
abilities to succeed under contrasting environmental conditions.
CAN WE LINK METAGENOME GENE CONTENT AND IRON SUPPLY IN THE OCEAN ?
TOULZA E.1,2, A. TAGLIABUE3, L. BOPP3, S. BLAIN1,4 AND G. PIGANEAU1,2
1
UPMC Univ Paris 06, FRE3355, BIOM, UMR7621, LOMIC, Observatoire Océanologique, F-66651
Banyuls/mer, France
2
CNRS, FRE3355, BIOM, Observatoire Océanologique, F-66651, Banyuls/mer, France
3
IPSL/Laboratoire des Sciences du Climat et de l’Environnement, CEN de Saclay, Bât. 701 l’Orme
des Merisiers, 91191 Gif-sur-Yvette, France
4
CNRS, UMR7621, LOMIC, Observatoire Océanologique, F-66651, Banyuls/mer, France
Iron is a rare ressouce in many oceanic areas and consequently its bioavilability often limits
the growth of marine microorganisms. To investigate the link between iron availability and sequence
prevalence in the environment, we performed a gene centric meta-analysis of available oceanic
metagenomic data. We listed 96 genes involved in iron metabolism from the literature to build a non
redundant database of 2357 sequences (limited to one per genus) corresponding to 8 metabolic
pathways: inorganic iron uptake, Heme-Fe metabolism, siderophore synthesis and uptake, storage of
iron, regulation, iron and oxidative stress. We used protein sequences of all available species (both
from GenBank and from the Moore foundation microbial isolates) to span the large phylogenetic
diversity of microorganisms. We performed a sequence similarity blast based search to identify the
genomic basis of iron uptake strategy in 72 metagenomic samples. Iron concentrations and other
environmental parameters of the sampling sites were estimated from ocean general circulation and
biogeochemistry model NEMO-PISCES. We used multivariate statistical analysis to relate the amount
and the prevalence of iron metabolism genes to environmental factors. This approach will provide new
insights into the structure and gene content adaptation of bacterial communities in response to iron
deprivation.
BACTERIAL
ASSEMBLAGE STRUCTURE AND CARBON METABOLISM ACROSS AN
LATITUDINAL TRANSECT
ATLANTIC
VARELA M. M.1,2, V. BALAGUÉ3, A. BODE1, A. CALVO-DÍAZ4, Á. CID2, J. GASOL3, E. MARAÑÓN5
4
AND X.-G. MORÁN
1
Centro Oceanográfico da Coruña, Instituto Español de Oceanografía. Paseo Marítimo Alcalde Fco.
Vázquez, 10 15001 A Coruña, Spain
2
Departamento de Biología Celular y Molecular, Universidade da Coruña, Rúa Alejandro de la Sota nº
1, 15008 A Coruña, Spain
3
Institut de Ciències del Mar-CMIMA, CSIC Departament de Biologia Marina i Oceanografia. Pg
Marítim de la Barceloneta 37-49, E08003 Barcelona, Cataluña, Spain
4
Centro Oceanográfico de Gijón, Instituto Español de Oceanografía, Avenida Príncipe de Asturias, 70
bis, 33212 Gijón, Spain
5
Departamento Ecoloxía e Bioloxía Animal, Universidade de Vigo, Campus Lagoas-Marcosende
36310-Vigo, Spain
Bacterioplankton contribute significantly to marine biogeochemical cycles, being responsible
for a large fraction of the respiration and dissolved organic matter (DOM) remineralisation in the
ocean. Nevertheless, little effort has been aimed at the study of the linkage between carbon processing
and the structure of the bacterial community. To investigate this issue, we conducted a set of dilution
culture experiments along a latitudinal transect (26ºN-34ºS) in the Atlantic Ocean during NovemberDecember 2007. We measured the latitudinal variability of empirical Leucine-to-carbon conversion
factor along with bacterial respiration. Furthermore, the phylogenetic composition of bacterioplankton
was followed in the time-series dilution cultures by using denaturing gradient gel electrophoresis
(DGGE) as well as fluorescence in situ hybridization (CARD-FISH). As expected, a rapid activation
of bacteria occurred during the experiments. Molecular techniques (DGGE) showed that the
community developed in the dilution culture was significantly different from that in the initial water
sample. In the original samples, CARD-FISH-detected cells were dominated by SAR11 type (31%),
whereas in the dilution culture Gammaproteobacteria (46%) dominated from day 2 onwards.
Empirical bacterial carbon-to-leucine (Leu) conversion factors ranged from 0.12-0.51 Kg C mol Leu-1
and did not show any latitudinal pattern. We found high percentages of Leu respiration, possibly
causing low conversion factors. Our study reveals that short-term changes in the bacterioplankton
community structure bacterial did not translated into large shifts in carbon use, at least in the range of
temperature found along the latitudinal transect.
COMPARISON
OF DIEL GENE EXPRESSION PROFILES IN AN OLIGOTROPHIC HIGH-ALTITUDE
LAKE AND TWO MARINE SYSTEMS THROUGH METRANSCRIPTOMICS
Vila-Costa M.1,2, S. Sharma1, M.A. Moran1 and E.O. Casamayor2
1
Department of Marine Sciences, University of Georgia, Athens, GA, USA
Department of Continental Ecology-Limnology, Centre d'Estudis Avançats de Blanes-CSIC, Acces
Cala St Francesc, 14, 17300 Blanes, Spain
2
Salinity is considered one of the main factors shaping bacterial community structure in aquatic
systems, and its influence may also be reflected at the genetic and functional levels. In this work, we
used metatranscriptomic sequencing to analyze day and night gene expression profiles of the bacterial
assemblages from the oligotrophic high altitude Lake Llebreta (1620 m above sea level) in the
Limnological Observatory of the Pyrenees (LOOP, Spanish Pyrenees, 42º 33’3”N, 0º 53’25”E). The
goal of the study was to obtain clues about the main biogeochemical processes carried out by bacteria
in a high altitude lake and explore unique biogeochemical features of this freshwater system. The
results for Lake Llebreta were compared with two previous diel metatranscriptomic studies of marine
systems, providing a perspective on ecosystems with greatly different salinity influences. We present
some first insights into common diel transcriptomics patterns among bacterioplankton communities
from marine and freshwater environments.
A NOVEL CLADE OF PROCHLOROCOCCUS FOUND IN HNLC WATERS IN THE SOUTH PACIFIC
OCEAN
WEST N.1,2, M. SUZUKI 1,3 AND P. LEBARON 1,3
1
UPMC Univ Paris 06, UMR 7621, LOMIC, UMS 2348, Observatoire Océanologique, F-66651
Banyuls/mer, France
2
CNRS, UMS 2348, Observatoire Océanologique, F-66651, Banyuls/mer, France
3
CNRS, UMR 7621, LOMIC, Observatoire Océanologique, F-66651, Banyuls/mer, France
The analysis of bacterial 16S rRNA gene clone libraries constructed from samples taken along
the BIOSOPE transect in the South Pacific Ocean revealed a novel cluster of Prochlorococcus only
present in two westerly stations close to the Marquesas islands (MAR) or in HNLC waters (HNL).
This cluster formed a separate sub-clade within the high light (HL)- adapted Prochlorococcus clade.
The abundance of this new clade and other HL-adapted clades was then determined along the
BIOSOPE transect and in other HNLC waters in the Equatorial Pacific by qPCR using specific
primers targeting the 16S-23S ITS region. The potential factors controlling the distribution of the new
clade in relation to other HL-adapted ecotypes of Prochlorococcus will be discussed.